From owner-chemistry@ccl.net Wed Jul 24 00:28:00 2013 From: "Karina Mu oz karina.munozbe|*|usach.cl" To: CCL Subject: CCL: ADF input from a Jaguar file Message-Id: <-48997-130723235238-29772-AiL5+4Mn3NxlFEIvxetlcA- -server.ccl.net> X-Original-From: "Karina Mu oz" Date: Tue, 23 Jul 2013 23:52:37 -0400 Sent to CCL by: "Karina Mu oz" [karina.munozbe%x%usach.cl] Dear colleagues Can I take as an ADF input file a Jaguar's output file with a resolved wave function (file.01.in) (unrestricted and broken symmetry calculation),to run an single point calculation in order to do a time-dependent calculation ? Thank you for your help. From owner-chemistry@ccl.net Wed Jul 24 01:03:00 2013 From: "kalyan onekalyan^yahoo.com" To: CCL Subject: CCL:G: Orbital plotting tools Message-Id: <-48998-130723133449-7104-kdWw+u8xlPskR7i+9T8E0g]^[server.ccl.net> X-Original-From: kalyan Content-Type: multipart/alternative; boundary="_0D29830C-6F8E-D44E-8BBB-71CCBA4D537C_" Date: Tue, 23 Jul 2013 19:34:37 +0200 MIME-Version: 1.0 Sent to CCL by: kalyan [onekalyan()yahoo.com] --_0D29830C-6F8E-D44E-8BBB-71CCBA4D537C_ Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Use cmd=20 Pop =3Dfull gfprint in gaussian. You may check in google=20 Best Regards=20 Kalyan -----Original Message----- > From: Susi Lehtola susi.lehtola]_[alumni.helsinki.fi Sent: 23/07/2013 19:19 To: Dhar, Kalyan kumar Subject: CCL:G: Orbital plotting tools Sent to CCL by: Susi Lehtola [susi.lehtola|a|alumni.helsinki.fi] Hi, I'm looking for a decent software that is able to produce orbital plots > from Gaussian-style formatted checkpoint or cube files. Moreover, I'm interested in software that can be scripted, so that manual labor involved in plotting hundreds of orbitals can be avoided. I've already had a look at Avogadro and IQmol, which don't support scripting. --=20 --------------------------------------------------------------- Mr. Susi Lehtola, PhD Postdoctoral researcher susi.lehtola[]alumni.helsinki.fi Department of Applied Physics http://www.helsinki.fi/~jzlehtol Aalto University Finland --------------------------------------------------------------- Susi Lehtola, FT Tutkijatohtori susi.lehtola[]alumni.helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Aalto-yliopisto --------------------------------------------------------------- -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt--_0D29830C-6F8E-D44E-8BBB-71CCBA4D537C_ Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="us-ascii"
Use cmd
Pop =3Dfull gfprint in gaussian.
You ma= y check in google

Best Regards
Kalyan
From: Susi Lehtola susi.lehtola]_[alumni.helsinki.fi
Se= nt: 23/07/2013 19:19
To: Dhar, Kalyan kumar Subject: CCL:G: Orbital plotting tools


Sent to CCL= by: Susi Lehtola [susi.lehtola|a|alumni.helsinki.fi]
Hi,


I'm= looking for a decent software that is able to produce orbital plots
>= ; from Gaussian-style formatted checkpoint or cube files. Moreover, I'm
= interested in software that can be scripted, so that manual labor
involv= ed in plotting hundreds of orbitals can be avoided.

I've already had= a look at Avogadro and IQmol, which don't support
scripting.
--
= ---------------------------------------------------------------
Mr. Susi= Lehtola, PhD          &n= bsp;  Postdoctoral researcher
susi.lehtola[]alumni.helsinki.fi = ;  Department of Applied Physics
http://www.helsinki.fi/~jzlehtol&n= bsp; Aalto University
        &n= bsp;            = ;             F= inland
---------------------------------------------------------------Susi Lehtola, FT         &nb= sp;        Tutkijatohtori
susi.lehtol= a[]alumni.helsinki.fi   Fysiikan laitos
http://www.helsinki.fi= /~jzlehtol  Aalto-yliopisto
---------------------------------------= ------------------------



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= --_0D29830C-6F8E-D44E-8BBB-71CCBA4D537C_-- From owner-chemistry@ccl.net Wed Jul 24 01:38:00 2013 From: "Belkhiri, lotfi lotfi.belkhiri^-^umc.edu.dz" To: CCL Subject: CCL:G: Orbital plotting tools Message-Id: <-48999-130723134719-14000-Nls8E6YQvCyos4L8WG9zDA:_:server.ccl.net> X-Original-From: "Belkhiri, lotfi" Content-Type: multipart/alternative; boundary=047d7bd7524431a06404e2314e4c Date: Tue, 23 Jul 2013 18:41:39 +0100 MIME-Version: 1.0 Sent to CCL by: "Belkhiri, lotfi" [lotfi.belkhiri++umc.edu.dz] --047d7bd7524431a06404e2314e4c Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Susi, You can use MOLELKEL, a free Molecular visualization tool which works rather well with various quantum chemistry programs. See the site web : http://molekel.cscs.ch/wiki/pmwiki.php/Main/DownloadBinary Best regards Lotfi 2013/7/23 Susi Lehtola susi.lehtola]_[alumni.helsinki.fi < owner-chemistry[-]ccl.net> > > Sent to CCL by: Susi Lehtola [susi.lehtola|a|alumni.helsinki.fi] > Hi, > > > I'm looking for a decent software that is able to produce orbital plots > > from Gaussian-style formatted checkpoint or cube files. Moreover, I'm > interested in software that can be scripted, so that manual labor > involved in plotting hundreds of orbitals can be avoided. > > I've already had a look at Avogadro and IQmol, which don't support > scripting. > -- > --------------------------------------------------------------- > Mr. Susi Lehtola, PhD Postdoctoral researcher > susi.lehtola[]alumni.helsinki.fi Department of Applied Physics > http://www.helsinki.fi/~jzlehtol Aalto University > Finland > --------------------------------------------------------------- > Susi Lehtola, FT Tutkijatohtori > susi.lehtola[]alumni.helsinki.fi Fysiikan laitos > http://www.helsinki.fi/~jzlehtol Aalto-yliopisto > --------------------------------------------------------------- > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Pr. Lotfi Belkhiri Directeur de Recherches - Groupe de Chimie Th=E9orique et Mod=E9lisation Unit=E9 de Recherche CHEMS - Universit=E9 Mentouri de Constantine jct9_cne2010[-]yahoo.fr Fax : +213 (0)31 68 15 45 Homepage : http://www.umc.edu.dz/vf/Labo/FacScienceExact/site_lacmom/crbst_21.html --047d7bd7524431a06404e2314e4c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Susi,

You can use MOLELKEL, a free M= olecular visualization tool which works rather well with various quantum ch= emistry programs.=A0
Best regards
Lotfi

2013/7/23 Susi Lehtola susi.lehtola]_[alumni.helsinki.fi &= lt;owner-chemi= stry[-]ccl.net>

Sent to CCL by: Susi Lehtola [susi.lehtola|a|alumni.helsinki.fi]
Hi,


I'm looking for a decent software that is able to produce orbital plots=
> from Gaussian-style formatted checkpoint or cube files. Moreover, I= 9;m
interested in software that can be scripted, so that manual labor
involved in plotting hundreds of orbitals can be avoided.

I've already had a look at Avogadro and IQmol, which don't support<= br> scripting.
--
---------------------------------------------------------------
Mr. Susi Lehtola, PhD =A0 =A0 =A0 =A0 =A0 =A0 Postdoctoral researcher
susi.lehtola[]alumn= i.helsinki.fi =A0 Department of Applied Physics
http://www.h= elsinki.fi/~jzlehtol =A0Aalto University
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Finland=
---------------------------------------------------------------
Susi Lehtola, FT =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Tutkijatohtori
susi.lehtola[]alumn= i.helsinki.fi =A0 Fysiikan laitos
http://www.h= elsinki.fi/~jzlehtol =A0Aalto-yliopisto
---------------------------------------------------------------



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--
Pr. Lotfi BelkhiriDirecteur de Recherches -=A0Groupe de Chimie Th=E9orique et Mod=E9lisatio= n
Unit=E9 de Recherche= CHEMS - Universit=E9 Mentouri de Constantine
jct9_cne2010[-]yahoo.fr
Fax : +213 (0)31 68 15 45
Homepage :=A0http://www.umc.edu.dz/vf/Labo/FacScienceExact/site_= lacmom/crbst_21.html
--047d7bd7524431a06404e2314e4c-- From owner-chemistry@ccl.net Wed Jul 24 02:13:00 2013 From: "Dr. Vitaly Chaban vvchaban__gmail.com" To: CCL Subject: CCL:G: Orbital plotting tools Message-Id: <-49000-130723141828-23555-HWNlAqDN70twZqtL+rdBHw~~server.ccl.net> X-Original-From: "Dr. Vitaly Chaban" Content-Type: multipart/alternative; boundary=047d7bf1985e609d7f04e231d182 Date: Tue, 23 Jul 2013 20:17:40 +0200 MIME-Version: 1.0 Sent to CCL by: "Dr. Vitaly Chaban" [vvchaban*o*gmail.com] --047d7bf1985e609d7f04e231d182 Content-Type: text/plain; charset=ISO-8859-1 VMD can plot orbitals and VMD can be scripted. Dr. Vitaly V. Chaban On Tue, Jul 23, 2013 at 4:18 PM, Susi Lehtola susi.lehtola]_[ alumni.helsinki.fi wrote: > > Sent to CCL by: Susi Lehtola [susi.lehtola|a|alumni.helsinki.fi] > Hi, > > > I'm looking for a decent software that is able to produce orbital plots > > from Gaussian-style formatted checkpoint or cube files. Moreover, I'm > interested in software that can be scripted, so that manual labor > involved in plotting hundreds of orbitals can be avoided. > > I've already had a look at Avogadro and IQmol, which don't support > scripting. > -- > --------------------------------------------------------------- > Mr. Susi Lehtola, PhD Postdoctoral researcher > susi.lehtola[]alumni.helsinki.fi Department of Applied Physics > http://www.helsinki.fi/~jzlehtol Aalto University > Finland > --------------------------------------------------------------- > Susi Lehtola, FT Tutkijatohtori > susi.lehtola[]alumni.helsinki.fi Fysiikan laitos > http://www.helsinki.fi/~jzlehtol Aalto-yliopisto > ---------------------------------------------------------------> > > --047d7bf1985e609d7f04e231d182 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
VMD can plot orbitals and VMD can be scripted.



<= div dir=3D"ltr">Dr. Vitaly V. Chaban


On Tue, Jul 23, 2013 at 4:18 PM, Susi Le= htola susi.lehtola]_[alumni.helsinki.= fi <owner-chemistry ~~ ccl.net> wrote:

Sent to CCL by: Susi Lehtola [susi.lehtola|a|alumni.helsinki.fi]
Hi,


I'm looking for a decent software that is able to produce orbital plots=
> from Gaussian-style formatted checkpoint or cube files. Moreover, I= 9;m
interested in software that can be scripted, so that manual labor
involved in plotting hundreds of orbitals can be avoided.

I've already had a look at Avogadro and IQmol, which don't support<= br> scripting.
--
---------------------------------------------------------------
Mr. Susi Lehtola, PhD =A0 =A0 =A0 =A0 =A0 =A0 Postdoctoral researcher
susi.lehtola[]alumn= i.helsinki.fi =A0 Department of Applied Physics
http://www.h= elsinki.fi/~jzlehtol =A0Aalto University
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Finland=
---------------------------------------------------------------
Susi Lehtola, FT =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Tutkijatohtori
susi.lehtola[]alumn= i.helsinki.fi =A0 Fysiikan laitos
http://www.h= elsinki.fi/~jzlehtol =A0Aalto-yliopisto
---------------------------------------------------------------



-=3D This is automatically added to each message by the mailing script =3D-=
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--047d7bf1985e609d7f04e231d182-- From owner-chemistry@ccl.net Wed Jul 24 02:48:00 2013 From: "Susi Lehtola susi.lehtola,,alumni.helsinki.fi" To: CCL Subject: CCL:G: Orbital plotting tools Message-Id: <-49001-130723164006-22132-JtNA8j9XeB1A/V7pffb/hA|server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Tue, 23 Jul 2013 23:39:54 +0300 Mime-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola..alumni.helsinki.fi] On Tue, 23 Jul 2013 17:18:40 +0300 "Susi Lehtola susi.lehtola]_[alumni.helsinki.fi" wrote: > Sent to CCL by: Susi Lehtola [susi.lehtola|a|alumni.helsinki.fi] > Hi, > > > I'm looking for a decent software that is able to produce orbital > plots > > from Gaussian-style formatted checkpoint or cube files. Moreover, > > I'm > interested in software that can be scripted, so that manual labor > involved in plotting hundreds of orbitals can be avoided. > > I've already had a look at Avogadro and IQmol, which don't support > scripting. Actually, I had a newer look at Jmol. In spite of the level of the documentation, I finally figured out how to plot cube file data, so there's no urgent need any more. -- --------------------------------------------------------------- Mr. Susi Lehtola, PhD Postdoctoral researcher susi.lehtola]-[alumni.helsinki.fi Department of Applied Physics http://www.helsinki.fi/~jzlehtol Aalto University Finland --------------------------------------------------------------- Susi Lehtola, FT Tutkijatohtori susi.lehtola]-[alumni.helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Aalto-yliopisto --------------------------------------------------------------- From owner-chemistry@ccl.net Wed Jul 24 06:26:00 2013 From: "Dan Maftei dan.maftei(a)uaic.ro" To: CCL Subject: CCL:G: What settings should I use in G09W to prevent the breaking of a bond? Message-Id: <-49002-130724054432-2061-TvREznn3QXqVEkOlQKy07Q]~[server.ccl.net> X-Original-From: Dan Maftei Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Wed, 24 Jul 2013 12:44:20 +0300 Mime-Version: 1.0 Sent to CCL by: Dan Maftei [dan.maftei[*]uaic.ro] Dear Gabriela, Your question appeared several times in the past on CCL. I am glad to see that you've already received a comprehensive answer (see Cina's response). Details below are proofing the same. At the theory level supplied in your input, geometry optimization (which completes on my machine in about 1 hour and 26 minutes + 21 minutes for computing vibrational frequencies) gives an equilibrium C-S internuclear distance of ~ 1.94 angstrom. This value is indeed larger than the sum of covalent radii (about 1.81 angstrom) and might make the molecular graphics program you are using to decide "I am not going to draw a cylinder (not a bond) between the two spheres". I have noticed the use of geom=connectivity in your input, and the corresponding parameters following geometry definition (though, it is incomplete, you should have 16 lines instead of 13). Although the option might be useful (see a response given by Ödön Farkas in 2006 on CCL, http://www.ccl.net/chemistry/resources/messages/2006/06/30.003-dir/), I never use it. It remembers me the ugliest bonds I've ever seen, when one of my students misused it in the input for a computational package that used (mandatory) atomic connectivity. Best wishes, Dan. On Mon, 22 Jul 2013 20:06:25 -0400 "gabriela arias gabriela.arias..yorkmail.cuny.edu" wrote: > > Sent to CCL by: "gabriela arias" [gabriela.arias-*-yorkmail.cuny.edu] > Hello everyone: > > I am doing an optimization and frequency calculation in Gaussian09 to > obtain the Raman and Infrared spectra of cysteine. In the output, the > bond between the thiol group and the adjacent carbon is broken, which > is wrong. What can I do to prevent this bond from breaking? These are > the settings that I am using: > > %nprocshared=2 > # opt=tight freq=raman b3lyp/6-311+g geom=connectivity > > Title Card Required > > -1 1 > C -2.18907515 2.08528252 -2.35362466 > C -2.51526953 1.22134909 -1.12122202 > O -2.82257852 1.77040643 -0.03142030 > N -0.74900832 2.37936285 -2.37861038 > H -0.23470752 1.52307575 -2.42622442 > H -0.53719378 2.94035858 -3.17887183 > O -2.46894955 -0.20480359 -1.21525919 > C -2.57949898 1.32244966 -3.63317742 > H -2.02919712 0.40622247 -3.68412445 > H -2.35285743 1.92271509 -4.48945717 > H -2.73937700 3.00150971 -2.30267762 > C -4.08814042 1.01436550 -3.60700190 > H -4.35940892 0.48434527 -4.49604181 > H -4.63844227 1.93059270 -3.55605487 > S -4.46517029 0.01579310 -2.18253651 > H -5.74849515 -0.24627848 -2.16027033 > > 1 2 1.0 4 1.0 8 1.0 11 1.0 > 2 3 2.0 7 1.0 > 3 > 4 5 1.0 6 1.0 > 5 > 6 > 7 > 8 9 1.0 10 1.0 12 1.0 > 9 > 10 > 11 > 12 13 1.0 14 1.0 15 1.0 > 13 > > Best regards and thanks for your help, > > Gabriela > > > > -= This is automatically added to each message by the mailing script > =- To recover the email address of the author of the message, please > change the strange characters on the top line to the -#- sign. You can > also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/> > From owner-chemistry@ccl.net Wed Jul 24 08:00:00 2013 From: "Steve Williams willsd---appstate.edu" To: CCL Subject: CCL: Single Point Calculation Not Converging Message-Id: <-49003-130724062826-25262-bFLYceU1kZeMs5aVxb2XOA*server.ccl.net> X-Original-From: Steve Williams Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Wed, 24 Jul 2013 06:28:03 -0400 Mime-Version: 1.0 (1.0) Sent to CCL by: Steve Williams [willsd*o*appstate.edu] Wow... You must have a BIG machine to even contemplate using a QZ basis with such a big molecule. I have had pretty good luck with the Dgauss basis sets, similar to Pople 6-31g** but optimized for solving atomic KS rather than atomic HF equations. Try DGDZVP with the DGA1 fitting set. Steve Williams Sent from my iPad On Jul 23, 2013, at 11:52 PM, "Bradley Welch bwelch5:_:slu.edu" wrote: > > Sent to CCL by: "Bradley Welch" [bwelch5^slu.edu] > Dear All, > > I am attempting to do a single point calculation on the experimental > configuration of a dimer from the crystal structure. I first attempted to use > a small basis set, and the pure functional BLYP. I used lanl2dz on the Co,N, > H, C, and O, and 6-31G* on the Cl. This calculation failed. I then scaled up > to QZVP since my first thought was those small basis sets were not flexible > enough for the problem. This calculation failed as well. I also ran it > without density fitting, but that seems to have not helped at all. Besides > using the QC algorithm in G09, what other options do I have available to get > this to converge? Would some sort of building up scheme be the best option? I > have no expectation any one will attempt to run this through your own > computers, but here is the geometry for reference, and the settings I used. > > #P BLYP/QZVP/QZVP scf=(conver=6) > > experimental geometry > > 0 1 > 27 5.002085847 5.527639519 3.769636231 > 17 2.775981352 5.742824793 3.450911304 > 17 5.546753961 3.315125693 3.901329243 > 7 5.924033679 6.059375512 2.056774986 > 7 7.367285171 7.017739534 0.538552372 > 7 5.329847859 6.600279690 5.476159302 > 7 5.628916118 8.190682272 6.981718950 > 8 7.992410500 6.757762124 4.087383042 > 8 7.220472773 9.928071865 0.016751237 > 8 5.882736218 10.116709493 4.825129579 > 8 7.549278914 9.813545786 9.131690524 > 6 5.540311097 5.774325339 0.711331232 > 6 4.473410144 4.979811059 0.381835999 > 1 3.859126438 4.546902992 1.015732800 > 6 4.246513234 4.796851429 -1.007364206 > 1 3.527710954 4.249846257 -1.320888541 > 6 5.129536800 5.327712653 -1.918643862 > 1 4.976995945 5.140184441 -2.876428185 > 6 6.212200256 6.141215741 -1.566836291 > 1 6.795373031 6.518924731 -2.189646747 > 6 6.379741752 6.271667542 -0.159858692 > 6 7.062037912 6.924128185 1.797355812 > 6 7.855453225 7.488696470 2.876591627 > 6 8.408420196 8.653596538 3.066796656 > 1 8.476585953 9.339403196 2.490968423 > 6 9.036221671 8.638557761 4.323484816 > 1 9.578333942 9.315788022 4.764173567 > 6 8.797552510 7.455617781 4.935914205 > 6 9.114843207 6.838967224 6.282960453 > 1 9.640525734 7.427288969 6.723441028 > 1 9.617140474 6.063666005 6.113289936 > 1 8.320796846 6.635830003 6.723346510 > 6 8.443256052 7.758533777 -0.099336545 > 1 8.878214897 7.254709403 -0.798582485 > 1 9.134483581 8.017438368 0.636198222 > 6 7.991736354 9.063272518 -0.716794079 > 6 8.123463108 9.526253294 -1.931202696 > 1 8.601822942 9.113404964 -2.673626264 > 6 7.463396364 10.840068634 -1.913221842 > 1 7.392018278 11.446942470 -2.698319207 > 6 7.006514398 10.984022095 -0.744299342 > 6 6.076473429 12.059683829 -0.186844583 > 1 5.940562627 12.790816725 -0.747644153 > 1 6.508438605 12.393163095 0.645607847 > 1 5.293794132 11.649869317 0.120246634 > 6 5.477736092 6.011069398 6.726417264 > 6 5.478849464 4.677047884 7.148806369 > 1 5.436191064 3.962625722 6.608309113 > 6 5.677829464 4.335773695 8.507904704 > 1 5.654313312 3.458777704 8.790046029 > 6 5.750707559 5.439454187 9.440596345 > 1 5.890759969 5.189993974 10.383390984 > 6 5.814237718 6.751734681 9.082420310 > 1 5.933671202 7.458874795 9.721758410 > 6 5.682694713 6.981782150 7.731808973 > 6 5.419022403 7.894567699 5.697568848 > 6 5.195478578 8.861443412 4.667418699 > 6 4.498452769 8.933642581 3.493283303 > 1 3.929991077 8.260361931 3.243455039 > 6 4.645736250 10.200269116 2.925951823 > 1 4.278773756 10.506328025 2.107154476 > 6 5.538905685 10.844249658 3.775817889 > 6 6.111700614 12.283006626 3.690195386 > 1 5.897147563 12.709706680 2.950172085 > 1 7.116130616 12.139044805 3.684531374 > 1 5.902181139 12.766313588 4.474706074 > 6 5.674480281 9.542153156 7.660702360 > 1 5.192471789 10.125687167 7.023651283 > 1 5.216127277 9.541459686 8.487633745 > 6 7.145210290 9.987642162 7.838999763 > 6 8.028668417 10.552104249 7.083290724 > 1 7.922985320 10.868278474 6.233110557 > 6 9.221774683 10.754249594 7.965688270 > 1 10.031752812 11.131834119 7.662147491 > 6 8.902972867 10.351545018 9.119819534 > 6 9.642903903 10.254134645 10.424869646 > 1 10.537195137 10.599571129 10.309738383 > 1 9.761768034 9.294885842 10.739370881 > 1 9.162129307 10.677801631 11.134509494 > 27 2.877414389 7.598002607 12.260829584 > 17 5.076996807 7.424383099 12.516765924 > 17 2.281502170 9.796256518 12.094466462 > 7 1.952797307 6.953534573 13.943619270 > 7 0.525865321 6.045931131 15.504106500 > 7 2.550167703 6.501577388 10.477582499 > 7 2.291295147 4.916333272 8.989998318 > 8 -0.134789408 6.386924003 11.970589278 > 8 0.591908871 3.157716510 15.962595004 > 8 1.962654620 2.978953678 11.178389063 > 8 0.194237522 3.275420766 6.863509088 > 6 2.306366041 7.388901708 15.250844444 > 6 3.413458621 8.155646453 15.651447671 > 1 4.010956547 8.562586504 14.975538228 > 6 3.612633001 8.333547764 16.940881809 > 1 4.309938891 8.853312146 17.328905422 > 6 2.761562682 7.774519705 17.966472115 > 1 2.841856052 7.976868162 18.831452782 > 6 1.622343042 6.993885174 17.545296100 > 1 1.088412665 6.593336084 18.111711793 > 6 1.456504667 6.801973874 16.148733162 > 6 0.830395129 6.254180958 14.158715927 > 6 -0.021812943 5.651391048 13.025286191 > 6 -0.620235679 4.421606331 12.976813723 > 1 -0.638085005 3.669896993 13.486953612 > 6 -1.170851985 4.472630296 11.636591740 > 1 -1.713443293 3.792468062 11.267257298 > 6 -0.892543886 5.646539067 11.104327598 > 6 -1.275391950 6.306419281 9.773947095 > 1 -1.787872517 5.729962116 9.274471352 > 1 -1.679213207 7.140530959 9.908860837 > 1 -0.440979317 6.457092259 9.277623117 > 6 -0.639069324 5.319034642 16.094740524 > 1 -0.989950910 5.862226174 16.752918343 > 1 -1.234994765 5.078858456 15.403253987 > 6 -0.064617146 4.093908675 16.716790370 > 6 -0.220772479 3.544304370 18.012050641 > 1 -0.733055092 3.986570661 18.616283855 > 6 0.425821649 2.258182130 17.922435093 > 1 0.471244655 1.654574994 18.662621366 > 6 0.893695721 2.108356575 16.796684152 > 6 1.728583214 1.096985675 16.170343932 > 1 1.895416019 0.382305766 16.758195416 > 1 1.354395066 0.650640505 15.352506543 > 1 2.628371432 1.471616836 15.868729962 > 6 2.357656655 7.104492030 9.289366565 > 6 2.366439959 8.426015676 8.838112721 > 1 2.470425971 9.122988904 9.449136744 > 6 2.181450698 8.689088557 7.454493003 > 1 2.218549373 9.584447907 7.148028971 > 6 2.007827071 7.628363483 6.590550216 > 1 1.968561839 7.933270679 5.654382158 > 6 2.044282172 6.353490560 6.943303150 > 1 1.876694612 5.672839855 6.356636578 > 6 2.191853895 6.123360881 8.318243329 > 6 2.456106617 5.213530597 10.310445730 > 6 2.669990175 4.194002381 11.340552735 > 6 3.377823281 4.215711635 12.477358237 > 1 3.924207954 4.815916857 12.820795833 > 6 3.203492349 2.886398776 13.047974548 > 1 3.615024603 2.572002796 13.878331158 > 6 2.354981994 2.216217400 12.259920146 > 6 1.646921395 0.866559886 12.258584813 > 1 2.026313010 0.411722858 13.143856688 > 1 0.781277169 0.950827057 12.306177086 > 1 1.935590075 0.433359728 11.510914001 > 6 2.147219720 3.523211592 8.349471974 > 1 2.661708055 2.926859771 8.937550033 > 1 2.584773502 3.592651357 7.551331747 > 6 0.734961031 3.098741994 8.109218860 > 6 -0.201240890 2.513278379 8.862315795 > 1 -0.042523805 2.243205588 9.809955560 > 6 -1.327777425 2.343464001 8.118178819 > 1 -2.091174002 2.013287589 8.359381223 > 6 -1.030184150 2.787991531 6.909908034 > 6 -1.792097118 2.922813975 5.619415598 > 1 -2.701670008 2.502836806 5.692255413 > 1 -1.820195348 3.802383476 5.315545842 > 1 -1.275371663 2.375694279 4.910314058 > > > Bradley Welch> > From owner-chemistry@ccl.net Wed Jul 24 08:35:00 2013 From: "Cory Pye cpye : ap.smu.ca" To: CCL Subject: CCL: Single Point Calculation Not Converging Message-Id: <-49004-130724072147-15748-AYvsoL/LYXZJFtwM9modyA|*|server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 24 Jul 2013 08:36:04 -0300 (ADT) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye|-|ap.smu.ca] Hello Bradley, I always start off with an HF/STO-3G calculation. I have found that it nearly always converges (the fewer the number of variables (MO coefficients), the easier the convergence). One can then use a guess=read at the basis set of interest, or use an intermediate level such as HF/3-21G or HF/6-31G*. I have a paper in the Central European Journal of Chemistry on this topic that might be helpful (C. C. Pye*, "An analysis of SCF and geometry covergence for diatomic molecules", Cent. Eur. J. Chem., 9, 567-571 (2011)) In your case, because of the transition metals, it might not converge to the correct state initially, so you may have to use guess=alter. -Cory Pye On Tue, 23 Jul 2013, Bradley Welch bwelch5:_:slu.edu wrote: > > Sent to CCL by: "Bradley Welch" [bwelch5^slu.edu] > Dear All, > > I am attempting to do a single point calculation on the experimental > configuration of a dimer from the crystal structure. I first attempted to use > a small basis set, and the pure functional BLYP. I used lanl2dz on the Co,N, > H, C, and O, and 6-31G* on the Cl. This calculation failed. I then scaled up > to QZVP since my first thought was those small basis sets were not flexible > enough for the problem. This calculation failed as well. I also ran it > without density fitting, but that seems to have not helped at all. Besides > using the QC algorithm in G09, what other options do I have available to get > this to converge? Would some sort of building up scheme be the best option? I > have no expectation any one will attempt to run this through your own > computers, but here is the geometry for reference, and the settings I used. > > #P BLYP/QZVP/QZVP scf=(conver=6) > > experimental geometry > > 0 1 > 27 5.002085847 5.527639519 3.769636231 > 17 2.775981352 5.742824793 3.450911304 > 17 5.546753961 3.315125693 3.901329243 > 7 5.924033679 6.059375512 2.056774986 > 7 7.367285171 7.017739534 0.538552372 > 7 5.329847859 6.600279690 5.476159302 > 7 5.628916118 8.190682272 6.981718950 > 8 7.992410500 6.757762124 4.087383042 > 8 7.220472773 9.928071865 0.016751237 > 8 5.882736218 10.116709493 4.825129579 > 8 7.549278914 9.813545786 9.131690524 > 6 5.540311097 5.774325339 0.711331232 > 6 4.473410144 4.979811059 0.381835999 > 1 3.859126438 4.546902992 1.015732800 > 6 4.246513234 4.796851429 -1.007364206 > 1 3.527710954 4.249846257 -1.320888541 > 6 5.129536800 5.327712653 -1.918643862 > 1 4.976995945 5.140184441 -2.876428185 > 6 6.212200256 6.141215741 -1.566836291 > 1 6.795373031 6.518924731 -2.189646747 > 6 6.379741752 6.271667542 -0.159858692 > 6 7.062037912 6.924128185 1.797355812 > 6 7.855453225 7.488696470 2.876591627 > 6 8.408420196 8.653596538 3.066796656 > 1 8.476585953 9.339403196 2.490968423 > 6 9.036221671 8.638557761 4.323484816 > 1 9.578333942 9.315788022 4.764173567 > 6 8.797552510 7.455617781 4.935914205 > 6 9.114843207 6.838967224 6.282960453 > 1 9.640525734 7.427288969 6.723441028 > 1 9.617140474 6.063666005 6.113289936 > 1 8.320796846 6.635830003 6.723346510 > 6 8.443256052 7.758533777 -0.099336545 > 1 8.878214897 7.254709403 -0.798582485 > 1 9.134483581 8.017438368 0.636198222 > 6 7.991736354 9.063272518 -0.716794079 > 6 8.123463108 9.526253294 -1.931202696 > 1 8.601822942 9.113404964 -2.673626264 > 6 7.463396364 10.840068634 -1.913221842 > 1 7.392018278 11.446942470 -2.698319207 > 6 7.006514398 10.984022095 -0.744299342 > 6 6.076473429 12.059683829 -0.186844583 > 1 5.940562627 12.790816725 -0.747644153 > 1 6.508438605 12.393163095 0.645607847 > 1 5.293794132 11.649869317 0.120246634 > 6 5.477736092 6.011069398 6.726417264 > 6 5.478849464 4.677047884 7.148806369 > 1 5.436191064 3.962625722 6.608309113 > 6 5.677829464 4.335773695 8.507904704 > 1 5.654313312 3.458777704 8.790046029 > 6 5.750707559 5.439454187 9.440596345 > 1 5.890759969 5.189993974 10.383390984 > 6 5.814237718 6.751734681 9.082420310 > 1 5.933671202 7.458874795 9.721758410 > 6 5.682694713 6.981782150 7.731808973 > 6 5.419022403 7.894567699 5.697568848 > 6 5.195478578 8.861443412 4.667418699 > 6 4.498452769 8.933642581 3.493283303 > 1 3.929991077 8.260361931 3.243455039 > 6 4.645736250 10.200269116 2.925951823 > 1 4.278773756 10.506328025 2.107154476 > 6 5.538905685 10.844249658 3.775817889 > 6 6.111700614 12.283006626 3.690195386 > 1 5.897147563 12.709706680 2.950172085 > 1 7.116130616 12.139044805 3.684531374 > 1 5.902181139 12.766313588 4.474706074 > 6 5.674480281 9.542153156 7.660702360 > 1 5.192471789 10.125687167 7.023651283 > 1 5.216127277 9.541459686 8.487633745 > 6 7.145210290 9.987642162 7.838999763 > 6 8.028668417 10.552104249 7.083290724 > 1 7.922985320 10.868278474 6.233110557 > 6 9.221774683 10.754249594 7.965688270 > 1 10.031752812 11.131834119 7.662147491 > 6 8.902972867 10.351545018 9.119819534 > 6 9.642903903 10.254134645 10.424869646 > 1 10.537195137 10.599571129 10.309738383 > 1 9.761768034 9.294885842 10.739370881 > 1 9.162129307 10.677801631 11.134509494 > 27 2.877414389 7.598002607 12.260829584 > 17 5.076996807 7.424383099 12.516765924 > 17 2.281502170 9.796256518 12.094466462 > 7 1.952797307 6.953534573 13.943619270 > 7 0.525865321 6.045931131 15.504106500 > 7 2.550167703 6.501577388 10.477582499 > 7 2.291295147 4.916333272 8.989998318 > 8 -0.134789408 6.386924003 11.970589278 > 8 0.591908871 3.157716510 15.962595004 > 8 1.962654620 2.978953678 11.178389063 > 8 0.194237522 3.275420766 6.863509088 > 6 2.306366041 7.388901708 15.250844444 > 6 3.413458621 8.155646453 15.651447671 > 1 4.010956547 8.562586504 14.975538228 > 6 3.612633001 8.333547764 16.940881809 > 1 4.309938891 8.853312146 17.328905422 > 6 2.761562682 7.774519705 17.966472115 > 1 2.841856052 7.976868162 18.831452782 > 6 1.622343042 6.993885174 17.545296100 > 1 1.088412665 6.593336084 18.111711793 > 6 1.456504667 6.801973874 16.148733162 > 6 0.830395129 6.254180958 14.158715927 > 6 -0.021812943 5.651391048 13.025286191 > 6 -0.620235679 4.421606331 12.976813723 > 1 -0.638085005 3.669896993 13.486953612 > 6 -1.170851985 4.472630296 11.636591740 > 1 -1.713443293 3.792468062 11.267257298 > 6 -0.892543886 5.646539067 11.104327598 > 6 -1.275391950 6.306419281 9.773947095 > 1 -1.787872517 5.729962116 9.274471352 > 1 -1.679213207 7.140530959 9.908860837 > 1 -0.440979317 6.457092259 9.277623117 > 6 -0.639069324 5.319034642 16.094740524 > 1 -0.989950910 5.862226174 16.752918343 > 1 -1.234994765 5.078858456 15.403253987 > 6 -0.064617146 4.093908675 16.716790370 > 6 -0.220772479 3.544304370 18.012050641 > 1 -0.733055092 3.986570661 18.616283855 > 6 0.425821649 2.258182130 17.922435093 > 1 0.471244655 1.654574994 18.662621366 > 6 0.893695721 2.108356575 16.796684152 > 6 1.728583214 1.096985675 16.170343932 > 1 1.895416019 0.382305766 16.758195416 > 1 1.354395066 0.650640505 15.352506543 > 1 2.628371432 1.471616836 15.868729962 > 6 2.357656655 7.104492030 9.289366565 > 6 2.366439959 8.426015676 8.838112721 > 1 2.470425971 9.122988904 9.449136744 > 6 2.181450698 8.689088557 7.454493003 > 1 2.218549373 9.584447907 7.148028971 > 6 2.007827071 7.628363483 6.590550216 > 1 1.968561839 7.933270679 5.654382158 > 6 2.044282172 6.353490560 6.943303150 > 1 1.876694612 5.672839855 6.356636578 > 6 2.191853895 6.123360881 8.318243329 > 6 2.456106617 5.213530597 10.310445730 > 6 2.669990175 4.194002381 11.340552735 > 6 3.377823281 4.215711635 12.477358237 > 1 3.924207954 4.815916857 12.820795833 > 6 3.203492349 2.886398776 13.047974548 > 1 3.615024603 2.572002796 13.878331158 > 6 2.354981994 2.216217400 12.259920146 > 6 1.646921395 0.866559886 12.258584813 > 1 2.026313010 0.411722858 13.143856688 > 1 0.781277169 0.950827057 12.306177086 > 1 1.935590075 0.433359728 11.510914001 > 6 2.147219720 3.523211592 8.349471974 > 1 2.661708055 2.926859771 8.937550033 > 1 2.584773502 3.592651357 7.551331747 > 6 0.734961031 3.098741994 8.109218860 > 6 -0.201240890 2.513278379 8.862315795 > 1 -0.042523805 2.243205588 9.809955560 > 6 -1.327777425 2.343464001 8.118178819 > 1 -2.091174002 2.013287589 8.359381223 > 6 -1.030184150 2.787991531 6.909908034 > 6 -1.792097118 2.922813975 5.619415598 > 1 -2.701670008 2.502836806 5.692255413 > 1 -1.820195348 3.802383476 5.315545842 > 1 -1.275371663 2.375694279 4.910314058 > > > Bradley Welch> > ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye!=!crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) From owner-chemistry@ccl.net Wed Jul 24 09:14:00 2013 From: "Mehboob Alam mehboob.cu]^[gmail.com" To: CCL Subject: CCL:G: Orbital plotting tools Message-Id: <-49005-130724035439-23695-NBZxECVtJgh6eQ7h2GwBpQ- -server.ccl.net> X-Original-From: Mehboob Alam Content-Type: multipart/alternative; boundary=bcaec51d2e544de7a204e23d3824 Date: Wed, 24 Jul 2013 13:24:32 +0530 MIME-Version: 1.0 Sent to CCL by: Mehboob Alam [mehboob.cu[-]gmail.com] --bcaec51d2e544de7a204e23d3824 Content-Type: text/plain; charset=ISO-8859-1 Hello Dr. Susi, You can use linux script to generate the cubefiles of different orbitals > from the formatted checkpoint file (I have done it also) Here is the command to do this *cubegen* *memory kind fchkfile cubefile npts format* You can get further information regarding this from the website: http://www.gaussian.com/g_tech/g_ur/u_cubegen.htm Hope it helps. Regards, Mehboob On Tue, Jul 23, 2013 at 11:47 PM, Dr. Vitaly Chaban vvchaban__gmail.com < owner-chemistry|*|ccl.net> wrote: > VMD can plot orbitals and VMD can be scripted. > > > > Dr. Vitaly V. Chaban > > > On Tue, Jul 23, 2013 at 4:18 PM, Susi Lehtola susi.lehtola]_[ > alumni.helsinki.fi wrote: > >> >> Sent to CCL by: Susi Lehtola [susi.lehtola|a|alumni.helsinki.fi] >> Hi, >> >> >> I'm looking for a decent software that is able to produce orbital plots >> > from Gaussian-style formatted checkpoint or cube files. Moreover, I'm >> interested in software that can be scripted, so that manual labor >> involved in plotting hundreds of orbitals can be avoided. >> >> I've already had a look at Avogadro and IQmol, which don't support >> scripting. >> -- >> --------------------------------------------------------------- >> Mr. Susi Lehtola, PhD Postdoctoral researcher >> susi.lehtola[]alumni.helsinki.fi Department of Applied Physics >> http://www.helsinki.fi/~jzlehtol Aalto University >> Finland >> --------------------------------------------------------------- >> Susi Lehtola, FT Tutkijatohtori >> susi.lehtola[]alumni.helsinki.fi Fysiikan laitos >> http://www.helsinki.fi/~jzlehtol Aalto-yliopisto >> ---------------------------------------------------------------** >> E-mail to subscribers: CHEMISTRY__ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST__ccl.net or use>> **>> >> >> > --bcaec51d2e544de7a204e23d3824 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello Dr. Susi,

You can use linux script to generate the cubefiles o= f different orbitals from the formatted checkpoint file (I have done it als= o)

Here is the command to do this

=A0cubegen memory kind fchkfile cubefile npts format=

You can get further information regarding this from the website: http://www.gaussian= .com/g_tech/g_ur/u_cubegen.htm

Hope it helps.

Regards, Mehboob


On Tue, Jul 23, 2013 at 11:47 PM, Dr. Vi= taly Chaban vvchab= an__gmail.com <owner-chemistry|*|ccl.net> wrote:
VMD can plot orbitals and V= MD can be scripted.



Dr. Vitaly V. Chaban


On Tue, Jul 23, 2013 at 4:18 PM, Su= si Lehtola susi.lehtola]_[alumni.helsinki.fi <owner-chemistry__ccl.net> wrote:

Sent to CCL by: Susi Lehtola [susi.lehtola|a|alumni.helsinki.fi]
Hi,


I'm looking for a decent software that is able to produce orbital plots=
> from Gaussian-style formatted checkpoint or cube files. Moreover, I= 9;m
interested in software that can be scripted, so that manual labor
involved in plotting hundreds of orbitals can be avoided.

I've already had a look at Avogadro and IQmol, which don't support<= br> scripting.
--
---------------------------------------------------------------
Mr. Susi Lehtola, PhD =A0 =A0 =A0 =A0 =A0 =A0 Postdoctoral researcher
susi.lehtola[]alumn= i.helsinki.fi =A0 Department of Applied Physics
http://www= .helsinki.fi/~jzlehtol =A0Aalto University
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Finland=
---------------------------------------------------------------
Susi Lehtola, FT =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Tutkijatohtori
susi.lehtola[]alumn= i.helsinki.fi =A0 Fysiikan laitos
http://www= .helsinki.fi/~jzlehtol =A0Aalto-yliopisto
---------------------------------------------------------------



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--bcaec51d2e544de7a204e23d3824-- From owner-chemistry@ccl.net Wed Jul 24 09:48:00 2013 From: "ranjita das ranjitadas.85[#]gmail.com" To: CCL Subject: CCL: ADF calcualtion Message-Id: <-49006-130724092920-21266-W3dMHl/Mpw0jKOEvsu7C2w-x-server.ccl.net> X-Original-From: ranjita das Content-Type: multipart/alternative; boundary=047d7b6d8d7c373c1c04e241e5ac Date: Wed, 24 Jul 2013 17:59:13 +0430 MIME-Version: 1.0 Sent to CCL by: ranjita das [ranjitadas.85^gmail.com] --047d7b6d8d7c373c1c04e241e5ac Content-Type: text/plain; charset=ISO-8859-1 Hi, the same problem I faced during the fragment analysis . you need not to give the job name, actually you have to save the input file in a folder which has no space in its name, and also save the input file with a name which do not have any space. I hope this will help you. regards On Sun, Jul 29, 2012 at 12:10 AM, Alex Fraser alex_fraser1984(0)yahoo.com < owner-chemistry::ccl.net> wrote: > > Sent to CCL by: "Alex Fraser" [alex_fraser1984[-]yahoo.com] > Dear All > I have tried to run fragment analysis in ADF. but when I define the > fragments > in "Region" and want to save the adf input file.an error "Fragment > analysis requires a job name (full name, including path)" arises. I don't > know where could I change the jobname. > Thanks in advance> > > -- Ranjita Das(SRF) C/O Prof. Pratim Kumar Chattaraj Department of Chemistry IIT Kharagpur Kharagpur:721302 --047d7b6d8d7c373c1c04e241e5ac Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi,
the same problem I faced during the= fragment analysis . you need not to give the job name, actually you have t= o save the input file in a folder which has no space in its name, and also = save the input file with a name which do not have any space. I hope this wi= ll help you.

regards


On Sun, Jul 29, 2012 at 12:10 AM, Alex Fraser alex_fraser1984= (0)yahoo.com <owner-chemistry::ccl.n= et> wrote:

Sent to CCL by: "Alex =A0 Fraser" [alex_fraser1984[-]yahoo.com]
Dear All
I have tried to run fragment analysis in ADF. but when I define the fragmen= ts
in "Region" and want to save the adf input file.an error "Fragment analysis requires a= job name (full name, including path)" arises. I don't know where = could I change the jobname.
Thanks in advance



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--
Ranjita Das(SRF)
C/O= Prof. Pratim Kumar Chattaraj
Department of Chemistry
IIT KharagpurKharagpur:721302
--047d7b6d8d7c373c1c04e241e5ac-- From owner-chemistry@ccl.net Wed Jul 24 10:24:00 2013 From: "ranjita das ranjitadas.85(!)gmail.com" To: CCL Subject: CCL:G: How to calculate the EDA using G09 mol files in ADF Message-Id: <-49007-130724095324-10356-zKXA+06zsVD+dFD7YGaHdg::server.ccl.net> X-Original-From: ranjita das Content-Type: multipart/alternative; boundary=089e013a132c60a54b04e2423b98 Date: Wed, 24 Jul 2013 18:23:18 +0430 MIME-Version: 1.0 Sent to CCL by: ranjita das [ranjitadas.85=-=gmail.com] --089e013a132c60a54b04e2423b98 Content-Type: text/plain; charset=ISO-8859-1 Hi everybody, I am recently using ADF package. for my systems, I have optimized them with G09 package. Now I want to carry out energy decomposition analysis using ADF. Now I want to now, if it is possible to perform this analysis with ADF importion the coordinates of the system from the Gaussian09 generated mol files (mol files of the G09 optimized structures), since G09 uses GTO whereas ADF uses STO. Thanks --089e013a132c60a54b04e2423b98 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi everybody,
I am recently using = ADF package. for my systems, I have optimized them with G09 package. Now I = want to carry out energy decomposi= tion analysis using ADF.
Now I want to now, if it is possible to perfo= rm this analysis with ADF importion the coordinates of the system from the = Gaussian09 generated mol files (mol files of the G09 optimized structures),= since G09 uses GTO whereas ADF uses STO.
Thanks
<= br>

--089e013a132c60a54b04e2423b98-- From owner-chemistry@ccl.net Wed Jul 24 13:41:01 2013 From: "Elaine Meng meng]*[cgl.ucsf.edu" To: CCL Subject: CCL:G: Orbital plotting tools Message-Id: <-49008-130724132505-1621-OaGWYa/oN2V+ngBrcEu8uA{=}server.ccl.net> X-Original-From: "Elaine Meng" Date: Wed, 24 Jul 2013 13:24:52 -0400 Sent to CCL by: "Elaine Meng" [meng_+_cgl.ucsf.edu] Hi Susi, Another possibility is Chimera. There is both a graphical interface (Volume Viewer) and command "volume" for setting contour levels, isosurface colors, and other display parameters of grid data such as electron density maps and electrostatic potential maps. It reads several formats including Gaussian cube. Chimera is free for noncommercial use, with downloads available for Windows, Mac, and Linux. http://www.rbvi.ucsf.edu/chimera/index.html More information on the volume viewer features: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From owner-chemistry@ccl.net Wed Jul 24 14:43:00 2013 From: "kalyan onekalyan.:.yahoo.com" To: CCL Subject: CCL: PCM and di-electric constant 12 Message-Id: <-49009-130724143610-16626-vU9Aq5IP8xdcuSOjgo3Vgg a server.ccl.net> X-Original-From: kalyan Content-Type: multipart/alternative; boundary="_8A5B7756-7F51-3083-EEE8-5A5E88D5D4B1_" Date: Wed, 24 Jul 2013 20:36:02 +0200 MIME-Version: 1.0 Sent to CCL by: kalyan [onekalyan .. yahoo.com] --_8A5B7756-7F51-3083-EEE8-5A5E88D5D4B1_ Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="Windows-1252" Can someone helping me how I will run my calc with sp. di- electric const 1= 2 in PCM calculations.(implicit solvation method) and RTIL=20 Best Regards=20 Kalyan= --_8A5B7756-7F51-3083-EEE8-5A5E88D5D4B1_ Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="Windows-1252"
Can someone helping me how I will run my calc wit= h sp. di- electric const 12 in PCM calculations.(implicit solvation method)= and RTIL

Best Regards
Kalyan
= --_8A5B7756-7F51-3083-EEE8-5A5E88D5D4B1_-- From owner-chemistry@ccl.net Wed Jul 24 15:18:00 2013 From: "Marcel Swart marcel.swart[#]icrea.cat" To: CCL Subject: CCL: Single Point Calculation Not Converging Message-Id: <-49010-130724091900-12201-xGRtYbUBxE/IxSvH9bIO1A|*|server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary="Apple-Mail=_C346F9DC-3D66-46A2-B905-E4DC4452CC9D" Date: Wed, 24 Jul 2013 15:18:20 +0200 Mime-Version: 1.0 (Mac OS X Mail 6.3 \(1503\)) Sent to CCL by: Marcel Swart [marcel.swart..icrea.cat] --Apple-Mail=_C346F9DC-3D66-46A2-B905-E4DC4452CC9D Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Dear Bradley, given that you're using the "experimental" structure, this will probably be one of the origins of your problems. I just had a look at your = structure, and the C-H distances are unusually short (0.91-0.94 =C5), e.g. ca. 0.15 = =C5 too short. This is a typical artefact of X-ray crystallography, where = they can not see the hydrogens, and use "riding models" (i.e. force fields!!) for the hydrogens. The C-H, O-H, N-H distances they then use are ridiculously short. There is a simple solution for that, simply open it with your favorite molecule editor, remove all hydrogens, and add them again automatically (*but* make sure that the correct number of = hydrogens is re-added, sometimes the programs make errors, especially for O and = N). Once you've done that, the SCF convergence will without any doubt go = better. (and if still not, then try e.g. the suggestions by Cory) Marcel PS. Assignment of hydrogens in crystal structures can have far-reaching effects, see e.g. M. Swart "A change in oxidation state of iron: scandium is not innocent" Chem. Commun. 2013, 49, 6650-6652 http://dx.doi.org/10.1039/C3CC42200C On 24 Jul 2013, at 13:36, "Cory Pye cpye : ap.smu.ca" = wrote: >=20 > Sent to CCL by: Cory Pye [cpye|-|ap.smu.ca] >=20 > Hello Bradley, > I always start off with an HF/STO-3G calculation. I have found that it = nearly > always converges (the fewer the number of variables (MO coefficients), = the > easier the convergence). One can then use a guess=3Dread at the basis = set of > interest, or use an intermediate level such as HF/3-21G or HF/6-31G*. > I have a paper in the Central European Journal of Chemistry on this = topic that > might be helpful (C. C. Pye*, "An analysis of SCF and geometry = covergence for > diatomic molecules", Cent. Eur. J. Chem., 9, 567-571 (2011)) > In your case, because of the transition metals, it might not converge = to the > correct state initially, so you may have to use guess=3Dalter. > -Cory Pye >=20 > On Tue, 23 Jul 2013, Bradley Welch bwelch5:_:slu.edu wrote: >=20 >>=20 >> Sent to CCL by: "Bradley Welch" [bwelch5^slu.edu] >> Dear All, >>=20 >> I am attempting to do a single point calculation on the experimental >> configuration of a dimer from the crystal structure. I first = attempted to use >> a small basis set, and the pure functional BLYP. I used lanl2dz on = the Co,N, >> H, C, and O, and 6-31G* on the Cl. This calculation failed. I then = scaled up >> to QZVP since my first thought was those small basis sets were not = flexible >> enough for the problem. This calculation failed as well. I also ran = it >> without density fitting, but that seems to have not helped at all. = Besides >> using the QC algorithm in G09, what other options do I have available = to get >> this to converge? Would some sort of building up scheme be the best = option? I >> have no expectation any one will attempt to run this through your own >> computers, but here is the geometry for reference, and the settings I = used. >>=20 >> #P BLYP/QZVP/QZVP scf=3D(conver=3D6) >>=20 >> experimental geometry >>=20 >> 0 1 >> 27 5.002085847 5.527639519 3.769636231 >> 17 2.775981352 5.742824793 3.450911304 >> 17 5.546753961 3.315125693 3.901329243 >> 7 5.924033679 6.059375512 2.056774986 >> 7 7.367285171 7.017739534 0.538552372 >> 7 5.329847859 6.600279690 5.476159302 >> 7 5.628916118 8.190682272 6.981718950 >> 8 7.992410500 6.757762124 4.087383042 >> 8 7.220472773 9.928071865 0.016751237 >> 8 5.882736218 10.116709493 4.825129579 >> 8 7.549278914 9.813545786 9.131690524 >> 6 5.540311097 5.774325339 0.711331232 >> 6 4.473410144 4.979811059 0.381835999 >> 1 3.859126438 4.546902992 1.015732800 >> 6 4.246513234 4.796851429 -1.007364206 >> 1 3.527710954 4.249846257 -1.320888541 >> 6 5.129536800 5.327712653 -1.918643862 >> 1 4.976995945 5.140184441 -2.876428185 >> 6 6.212200256 6.141215741 -1.566836291 >> 1 6.795373031 6.518924731 -2.189646747 >> 6 6.379741752 6.271667542 -0.159858692 >> 6 7.062037912 6.924128185 1.797355812 >> 6 7.855453225 7.488696470 2.876591627 >> 6 8.408420196 8.653596538 3.066796656 >> 1 8.476585953 9.339403196 2.490968423 >> 6 9.036221671 8.638557761 4.323484816 >> 1 9.578333942 9.315788022 4.764173567 >> 6 8.797552510 7.455617781 4.935914205 >> 6 9.114843207 6.838967224 6.282960453 >> 1 9.640525734 7.427288969 6.723441028 >> 1 9.617140474 6.063666005 6.113289936 >> 1 8.320796846 6.635830003 6.723346510 >> 6 8.443256052 7.758533777 -0.099336545 >> 1 8.878214897 7.254709403 -0.798582485 >> 1 9.134483581 8.017438368 0.636198222 >> 6 7.991736354 9.063272518 -0.716794079 >> 6 8.123463108 9.526253294 -1.931202696 >> 1 8.601822942 9.113404964 -2.673626264 >> 6 7.463396364 10.840068634 -1.913221842 >> 1 7.392018278 11.446942470 -2.698319207 >> 6 7.006514398 10.984022095 -0.744299342 >> 6 6.076473429 12.059683829 -0.186844583 >> 1 5.940562627 12.790816725 -0.747644153 >> 1 6.508438605 12.393163095 0.645607847 >> 1 5.293794132 11.649869317 0.120246634 >> 6 5.477736092 6.011069398 6.726417264 >> 6 5.478849464 4.677047884 7.148806369 >> 1 5.436191064 3.962625722 6.608309113 >> 6 5.677829464 4.335773695 8.507904704 >> 1 5.654313312 3.458777704 8.790046029 >> 6 5.750707559 5.439454187 9.440596345 >> 1 5.890759969 5.189993974 10.383390984 >> 6 5.814237718 6.751734681 9.082420310 >> 1 5.933671202 7.458874795 9.721758410 >> 6 5.682694713 6.981782150 7.731808973 >> 6 5.419022403 7.894567699 5.697568848 >> 6 5.195478578 8.861443412 4.667418699 >> 6 4.498452769 8.933642581 3.493283303 >> 1 3.929991077 8.260361931 3.243455039 >> 6 4.645736250 10.200269116 2.925951823 >> 1 4.278773756 10.506328025 2.107154476 >> 6 5.538905685 10.844249658 3.775817889 >> 6 6.111700614 12.283006626 3.690195386 >> 1 5.897147563 12.709706680 2.950172085 >> 1 7.116130616 12.139044805 3.684531374 >> 1 5.902181139 12.766313588 4.474706074 >> 6 5.674480281 9.542153156 7.660702360 >> 1 5.192471789 10.125687167 7.023651283 >> 1 5.216127277 9.541459686 8.487633745 >> 6 7.145210290 9.987642162 7.838999763 >> 6 8.028668417 10.552104249 7.083290724 >> 1 7.922985320 10.868278474 6.233110557 >> 6 9.221774683 10.754249594 7.965688270 >> 1 10.031752812 11.131834119 7.662147491 >> 6 8.902972867 10.351545018 9.119819534 >> 6 9.642903903 10.254134645 10.424869646 >> 1 10.537195137 10.599571129 10.309738383 >> 1 9.761768034 9.294885842 10.739370881 >> 1 9.162129307 10.677801631 11.134509494 >> 27 2.877414389 7.598002607 12.260829584 >> 17 5.076996807 7.424383099 12.516765924 >> 17 2.281502170 9.796256518 12.094466462 >> 7 1.952797307 6.953534573 13.943619270 >> 7 0.525865321 6.045931131 15.504106500 >> 7 2.550167703 6.501577388 10.477582499 >> 7 2.291295147 4.916333272 8.989998318 >> 8 -0.134789408 6.386924003 11.970589278 >> 8 0.591908871 3.157716510 15.962595004 >> 8 1.962654620 2.978953678 11.178389063 >> 8 0.194237522 3.275420766 6.863509088 >> 6 2.306366041 7.388901708 15.250844444 >> 6 3.413458621 8.155646453 15.651447671 >> 1 4.010956547 8.562586504 14.975538228 >> 6 3.612633001 8.333547764 16.940881809 >> 1 4.309938891 8.853312146 17.328905422 >> 6 2.761562682 7.774519705 17.966472115 >> 1 2.841856052 7.976868162 18.831452782 >> 6 1.622343042 6.993885174 17.545296100 >> 1 1.088412665 6.593336084 18.111711793 >> 6 1.456504667 6.801973874 16.148733162 >> 6 0.830395129 6.254180958 14.158715927 >> 6 -0.021812943 5.651391048 13.025286191 >> 6 -0.620235679 4.421606331 12.976813723 >> 1 -0.638085005 3.669896993 13.486953612 >> 6 -1.170851985 4.472630296 11.636591740 >> 1 -1.713443293 3.792468062 11.267257298 >> 6 -0.892543886 5.646539067 11.104327598 >> 6 -1.275391950 6.306419281 9.773947095 >> 1 -1.787872517 5.729962116 9.274471352 >> 1 -1.679213207 7.140530959 9.908860837 >> 1 -0.440979317 6.457092259 9.277623117 >> 6 -0.639069324 5.319034642 16.094740524 >> 1 -0.989950910 5.862226174 16.752918343 >> 1 -1.234994765 5.078858456 15.403253987 >> 6 -0.064617146 4.093908675 16.716790370 >> 6 -0.220772479 3.544304370 18.012050641 >> 1 -0.733055092 3.986570661 18.616283855 >> 6 0.425821649 2.258182130 17.922435093 >> 1 0.471244655 1.654574994 18.662621366 >> 6 0.893695721 2.108356575 16.796684152 >> 6 1.728583214 1.096985675 16.170343932 >> 1 1.895416019 0.382305766 16.758195416 >> 1 1.354395066 0.650640505 15.352506543 >> 1 2.628371432 1.471616836 15.868729962 >> 6 2.357656655 7.104492030 9.289366565 >> 6 2.366439959 8.426015676 8.838112721 >> 1 2.470425971 9.122988904 9.449136744 >> 6 2.181450698 8.689088557 7.454493003 >> 1 2.218549373 9.584447907 7.148028971 >> 6 2.007827071 7.628363483 6.590550216 >> 1 1.968561839 7.933270679 5.654382158 >> 6 2.044282172 6.353490560 6.943303150 >> 1 1.876694612 5.672839855 6.356636578 >> 6 2.191853895 6.123360881 8.318243329 >> 6 2.456106617 5.213530597 10.310445730 >> 6 2.669990175 4.194002381 11.340552735 >> 6 3.377823281 4.215711635 12.477358237 >> 1 3.924207954 4.815916857 12.820795833 >> 6 3.203492349 2.886398776 13.047974548 >> 1 3.615024603 2.572002796 13.878331158 >> 6 2.354981994 2.216217400 12.259920146 >> 6 1.646921395 0.866559886 12.258584813 >> 1 2.026313010 0.411722858 13.143856688 >> 1 0.781277169 0.950827057 12.306177086 >> 1 1.935590075 0.433359728 11.510914001 >> 6 2.147219720 3.523211592 8.349471974 >> 1 2.661708055 2.926859771 8.937550033 >> 1 2.584773502 3.592651357 7.551331747 >> 6 0.734961031 3.098741994 8.109218860 >> 6 -0.201240890 2.513278379 8.862315795 >> 1 -0.042523805 2.243205588 9.809955560 >> 6 -1.327777425 2.343464001 8.118178819 >> 1 -2.091174002 2.013287589 8.359381223 >> 6 -1.030184150 2.787991531 6.909908034 >> 6 -1.792097118 2.922813975 5.619415598 >> 1 -2.701670008 2.502836806 5.692255413 >> 1 -1.820195348 3.802383476 5.315545842 >> 1 -1.275371663 2.375694279 4.910314058 >>=20 >>=20 >> Bradley Welch> >>=20 >=20 > ************* ! Dr. Cory C. Pye > ***************** ! Associate Professor > *** ** ** ** ! Theoretical and Computational Chemistry > ** * **** ! Department of Chemistry, Saint Mary's = University > ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 > ** * * ! cpye-$-crux.stmarys.ca = http://apwww.stmarys.ca/~cpye > *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 > ***************** ! > ************* ! Les Hartree-Focks (Apologies to Montreal = Canadien Fans) >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D dr. Marcel Swart ICREA Research Professor at Institut de Qu=EDmica Computacional i Cat=E0lisi Universitat de Girona Facultat de Ci=E8ncies Campus Montilivi 17071 Girona Catalunya (Spain) tel +34-972-418861 fax +34-972-418356 e-mail marcel.swart__icrea.cat marcel.swart__udg.edu web http://www.marcelswart.eu vCard addressbook://www.marcelswart.eu/MSwart.vcf =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D --Apple-Mail=_C346F9DC-3D66-46A2-B905-E4DC4452CC9D Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1 Dear = Bradley,

given that you're using the "experimental" = structure, this will probably
be one of the origins of your = problems. I just had a look at your structure,
and the C-H = distances are unusually short (0.91-0.94 =C5), e.g. ca. 0.15 = =C5
too short. This is a typical artefact of X-ray = crystallography, where they
can not see the hydrogens, and use = "riding models" (i.e. force fields!!)
for the hydrogens. The = C-H, O-H, N-H distances they then use are
ridiculously short. = There is a simple solution for that, simply open it
with your = favorite molecule editor, remove all hydrogens, and add = them
again automatically (*but* make sure that the correct = number of hydrogens
is re-added, sometimes the programs make = errors, especially for O and N).
Once you've done that, the = SCF convergence will without any doubt go better.
(and if = still not, then try e.g. the suggestions by = Cory)

Marcel

PS.
Assignment of hydrogens in crystal structures can have = far-reaching
effects, see e.g.
M. Swart
"A change = in oxidation state of iron: scandium is not innocent"
Chem. = Commun. 2013, 49, 6650-6652

On 24 Jul 2013, at 13:36, "Cory Pye = cpye : ap.smu.ca" <owner-chemistry__ccl.net> = wrote:


Sent to CCL by: Cory Pye [cpye|-|ap.smu.ca]

Hello Bradley,
I = always start off with an HF/STO-3G calculation. I have found that it = nearly
always converges (the fewer the number of variables (MO = coefficients), the
easier the convergence). One can then use a = guess=3Dread at the basis set of
interest, or use an intermediate = level such as HF/3-21G or HF/6-31G*.
I have a paper in the Central = European Journal of Chemistry on this topic that
might be helpful (C. = C. Pye*, "An analysis of SCF and geometry covergence for
diatomic = molecules", Cent. Eur. J. Chem., 9, 567-571 (2011))
In your case, = because of the transition metals, it might not converge to = the
correct state initially, so you may have to use = guess=3Dalter.
-Cory Pye

On Tue, 23 Jul 2013, Bradley Welch = bwelch5:_:slu.edu = wrote:


Sent to CCL by: "Bradley =  Welch" [bwelch5^slu.edu]
Dear = All,

I am attempting to do a single point calculation on the = experimental
configuration of a dimer from the crystal structure. I = first attempted to use
a small basis set, and the pure functional = BLYP. I used lanl2dz on the Co,N,
H, C, and O, and 6-31G* on the Cl. = This calculation failed. I then scaled up
to QZVP since my first = thought was those small basis sets were not flexible
enough for the = problem. This calculation failed as well. I also ran it
without = density fitting, but that seems to have not helped at all. = Besides
using the QC algorithm in G09, what other options do I have = available to get
this to converge? Would some sort of building up = scheme be the best option? I
have no expectation any one will attempt = to run this through your own
computers, but here is the geometry for = reference, and the settings I used.

#P BLYP/QZVP/QZVP = scf=3D(conver=3D6)

experimental geometry

0 1
27 =       5.002085847 =      5.527639519 =      3.769636231
17 =       2.775981352 =      5.742824793 =      3.450911304
17 =       5.546753961 =      3.315125693 =      3.901329243
7 =        5.924033679 =      6.059375512 =      2.056774986
7 =        7.367285171 =      7.017739534 =      0.538552372
7 =        5.329847859 =      6.600279690 =      5.476159302
7 =        5.628916118 =      8.190682272 =      6.981718950
8 =        7.992410500 =      6.757762124 =      4.087383042
8 =        7.220472773 =      9.928071865 =      0.016751237
8 =        5.882736218 =     10.116709493 =      4.825129579
8 =        7.549278914 =      9.813545786 =      9.131690524
6 =        5.540311097 =      5.774325339 =      0.711331232
6 =        4.473410144 =      4.979811059 =      0.381835999
1 =        3.859126438 =      4.546902992 =      1.015732800
6 =        4.246513234 =      4.796851429 =     -1.007364206
1 =        3.527710954 =      4.249846257 =     -1.320888541
6 =        5.129536800 =      5.327712653 =     -1.918643862
1 =        4.976995945 =      5.140184441 =     -2.876428185
6 =        6.212200256 =      6.141215741 =     -1.566836291
1 =        6.795373031 =      6.518924731 =     -2.189646747
6 =        6.379741752 =      6.271667542 =     -0.159858692
6 =        7.062037912 =      6.924128185 =      1.797355812
6 =        7.855453225 =      7.488696470 =      2.876591627
6 =        8.408420196 =      8.653596538 =      3.066796656
1 =        8.476585953 =      9.339403196 =      2.490968423
6 =        9.036221671 =      8.638557761 =      4.323484816
1 =        9.578333942 =      9.315788022 =      4.764173567
6 =        8.797552510 =      7.455617781 =      4.935914205
6 =        9.114843207 =      6.838967224 =      6.282960453
1 =        9.640525734 =      7.427288969 =      6.723441028
1 =        9.617140474 =      6.063666005 =      6.113289936
1 =        8.320796846 =      6.635830003 =      6.723346510
6 =        8.443256052 =      7.758533777 =     -0.099336545
1 =        8.878214897 =      7.254709403 =     -0.798582485
1 =        9.134483581 =      8.017438368 =      0.636198222
6 =        7.991736354 =      9.063272518 =     -0.716794079
6 =        8.123463108 =      9.526253294 =     -1.931202696
1 =        8.601822942 =      9.113404964 =     -2.673626264
6 =        7.463396364 =     10.840068634 =     -1.913221842
1 =        7.392018278 =     11.446942470 =     -2.698319207
6 =        7.006514398 =     10.984022095 =     -0.744299342
6 =        6.076473429 =     12.059683829 =     -0.186844583
1 =        5.940562627 =     12.790816725 =     -0.747644153
1 =        6.508438605 =     12.393163095 =      0.645607847
1 =        5.293794132 =     11.649869317 =      0.120246634
6 =        5.477736092 =      6.011069398 =      6.726417264
6 =        5.478849464 =      4.677047884 =      7.148806369
1 =        5.436191064 =      3.962625722 =      6.608309113
6 =        5.677829464 =      4.335773695 =      8.507904704
1 =        5.654313312 =      3.458777704 =      8.790046029
6 =        5.750707559 =      5.439454187 =      9.440596345
1 =        5.890759969 =      5.189993974 =     10.383390984
6 =        5.814237718 =      6.751734681 =      9.082420310
1 =        5.933671202 =      7.458874795 =      9.721758410
6 =        5.682694713 =      6.981782150 =      7.731808973
6 =        5.419022403 =      7.894567699 =      5.697568848
6 =        5.195478578 =      8.861443412 =      4.667418699
6 =        4.498452769 =      8.933642581 =      3.493283303
1 =        3.929991077 =      8.260361931 =      3.243455039
6 =        4.645736250 =     10.200269116 =      2.925951823
1 =        4.278773756 =     10.506328025 =      2.107154476
6 =        5.538905685 =     10.844249658 =      3.775817889
6 =        6.111700614 =     12.283006626 =      3.690195386
1 =        5.897147563 =     12.709706680 =      2.950172085
1 =        7.116130616 =     12.139044805 =      3.684531374
1 =        5.902181139 =     12.766313588 =      4.474706074
6 =        5.674480281 =      9.542153156 =      7.660702360
1 =        5.192471789 =     10.125687167 =      7.023651283
1 =        5.216127277 =      9.541459686 =      8.487633745
6 =        7.145210290 =      9.987642162 =      7.838999763
6 =        8.028668417 =     10.552104249 =      7.083290724
1 =        7.922985320 =     10.868278474 =      6.233110557
6 =        9.221774683 =     10.754249594 =      7.965688270
1 =       10.031752812 =     11.131834119 =      7.662147491
6 =        8.902972867 =     10.351545018 =      9.119819534
6 =        9.642903903 =     10.254134645 =     10.424869646
1 =       10.537195137 =     10.599571129 =     10.309738383
1 =        9.761768034 =      9.294885842 =     10.739370881
1 =        9.162129307 =     10.677801631 =     11.134509494
27 =       2.877414389 =      7.598002607 =     12.260829584
17 =       5.076996807 =      7.424383099 =     12.516765924
17 =       2.281502170 =      9.796256518 =     12.094466462
7 =        1.952797307 =      6.953534573 =     13.943619270
7 =        0.525865321 =      6.045931131 =     15.504106500
7 =        2.550167703 =      6.501577388 =     10.477582499
7 =        2.291295147 =      4.916333272 =      8.989998318
8 =       -0.134789408 =      6.386924003 =     11.970589278
8 =        0.591908871 =      3.157716510 =     15.962595004
8 =        1.962654620 =      2.978953678 =     11.178389063
8 =        0.194237522 =      3.275420766 =      6.863509088
6 =        2.306366041 =      7.388901708 =     15.250844444
6 =        3.413458621 =      8.155646453 =     15.651447671
1 =        4.010956547 =      8.562586504 =     14.975538228
6 =        3.612633001 =      8.333547764 =     16.940881809
1 =        4.309938891 =      8.853312146 =     17.328905422
6 =        2.761562682 =      7.774519705 =     17.966472115
1 =        2.841856052 =      7.976868162 =     18.831452782
6 =        1.622343042 =      6.993885174 =     17.545296100
1 =        1.088412665 =      6.593336084 =     18.111711793
6 =        1.456504667 =      6.801973874 =     16.148733162
6 =        0.830395129 =      6.254180958 =     14.158715927
6 =       -0.021812943 =      5.651391048 =     13.025286191
6 =       -0.620235679 =      4.421606331 =     12.976813723
1 =       -0.638085005 =      3.669896993 =     13.486953612
6 =       -1.170851985 =      4.472630296 =     11.636591740
1 =       -1.713443293 =      3.792468062 =     11.267257298
6 =       -0.892543886 =      5.646539067 =     11.104327598
6 =       -1.275391950 =      6.306419281 =      9.773947095
1 =       -1.787872517 =      5.729962116 =      9.274471352
1 =       -1.679213207 =      7.140530959 =      9.908860837
1 =       -0.440979317 =      6.457092259 =      9.277623117
6 =       -0.639069324 =      5.319034642 =     16.094740524
1 =       -0.989950910 =      5.862226174 =     16.752918343
1 =       -1.234994765 =      5.078858456 =     15.403253987
6 =       -0.064617146 =      4.093908675 =     16.716790370
6 =       -0.220772479 =      3.544304370 =     18.012050641
1 =       -0.733055092 =      3.986570661 =     18.616283855
6 =        0.425821649 =      2.258182130 =     17.922435093
1 =        0.471244655 =      1.654574994 =     18.662621366
6 =        0.893695721 =      2.108356575 =     16.796684152
6 =        1.728583214 =      1.096985675 =     16.170343932
1 =        1.895416019 =      0.382305766 =     16.758195416
1 =        1.354395066 =      0.650640505 =     15.352506543
1 =        2.628371432 =      1.471616836 =     15.868729962
6 =        2.357656655 =      7.104492030 =      9.289366565
6 =        2.366439959 =      8.426015676 =      8.838112721
1 =        2.470425971 =      9.122988904 =      9.449136744
6 =        2.181450698 =      8.689088557 =      7.454493003
1 =        2.218549373 =      9.584447907 =      7.148028971
6 =        2.007827071 =      7.628363483 =      6.590550216
1 =        1.968561839 =      7.933270679 =      5.654382158
6 =        2.044282172 =      6.353490560 =      6.943303150
1 =        1.876694612 =      5.672839855 =      6.356636578
6 =        2.191853895 =      6.123360881 =      8.318243329
6 =        2.456106617 =      5.213530597 =     10.310445730
6 =        2.669990175 =      4.194002381 =     11.340552735
6 =        3.377823281 =      4.215711635 =     12.477358237
1 =        3.924207954 =      4.815916857 =     12.820795833
6 =        3.203492349 =      2.886398776 =     13.047974548
1 =        3.615024603 =      2.572002796 =     13.878331158
6 =        2.354981994 =      2.216217400 =     12.259920146
6 =        1.646921395 =      0.866559886 =     12.258584813
1 =        2.026313010 =      0.411722858 =     13.143856688
1 =        0.781277169 =      0.950827057 =     12.306177086
1 =        1.935590075 =      0.433359728 =     11.510914001
6 =        2.147219720 =      3.523211592 =      8.349471974
1 =        2.661708055 =      2.926859771 =      8.937550033
1 =        2.584773502 =      3.592651357 =      7.551331747
6 =        0.734961031 =      3.098741994 =      8.109218860
6 =       -0.201240890 =      2.513278379 =      8.862315795
1 =       -0.042523805 =      2.243205588 =      9.809955560
6 =       -1.327777425 =      2.343464001 =      8.118178819
1 =       -2.091174002 =      2.013287589 =      8.359381223
6 =       -1.030184150 =      2.787991531 =      6.909908034
6 =       -1.792097118 =      2.922813975 =      5.619415598
1 =       -2.701670008 =      2.502836806 =      5.692255413
1 =       -1.820195348 =      3.802383476 =      5.315545842
1 =       -1.275371663 =      2.375694279 =      4.910314058


Bradley = Welch>


  ************* =    !  Dr. Cory C. Pye
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= --Apple-Mail=_C346F9DC-3D66-46A2-B905-E4DC4452CC9D-- From owner-chemistry@ccl.net Wed Jul 24 15:53:00 2013 From: "Renier Dreyer renier.dreyer[#]crunchyard.com" To: CCL Subject: CCL: LAMMPS now available on CrunchYard Message-Id: <-49011-130724095258-9918-xOhILuT4mDVbU8zQKD0/gA:+:server.ccl.net> X-Original-From: "Renier Dreyer" Date: Wed, 24 Jul 2013 09:52:54 -0400 Sent to CCL by: "Renier Dreyer" [renier.dreyer**crunchyard.com] CrunchYard has added the classical molecular dynamics code, Large-scale Atomic Molecular Massively Parallel Simulator (LAMMPS) to our system. Computational chemists around the world can now cut out the middleman, running their own simulations securely and cost-effectively via the internet, on a pay per use basis. LAMMPS is a parallel particle simulator at the atomic, meso, or continuum scale and is often used to model atoms. LAMMPS has the potential to handle soft materials (including biomolecules and polymers) and solid-state materials (like metals and semiconductors). It can be used for simulations involving coarse- grained or mesoscopic systems. For cost-efficient, time-efficient, secure and middle-man free simulations using LAMMPS, register at www.crunchyard.com or contact Dr Renier Dreyer at +27 11 717 6379 or renier.dreyer:+:crunchyard.com From owner-chemistry@ccl.net Wed Jul 24 16:28:01 2013 From: "Pratima Satish ps544- -cornell.edu" To: CCL Subject: CCL:G: Gaussian 09: how to fragment molecules Message-Id: <-49012-130724101444-28926-XbMpU7owIELDtdQTjohdrw*server.ccl.net> X-Original-From: "Pratima Satish" Date: Wed, 24 Jul 2013 10:14:43 -0400 Sent to CCL by: "Pratima Satish" [ps544^cornell.edu] Hi, I am trying to define a transition metal complex in Gaussian 09 with localised charges - for instance, a hexaaquairon complex [Fe(H2O)6]2+, where the iron centre specifically has a +2 charge and all the water ligands have 0 charge. However, I am not fully sure as to how to use the Guess=Fragment feature in Gaussian, which keeps giving me the following error message: "This type of calculation cannot be archived." I am including my input file: ------------------------- #n UB3LYP/Gen Opt Guess=(Only,Fragment=7) Hexaaquairon(2) bond length 2.0 A high spin (multiplicity 5) fragmented into Fe2+ and 6 waters 2 5, 2 5, 0 1, 0 1, 0 1, 0 1, 0 1, 0 1 Fe(Fragment=1) 0.000000 0.000007 0.000000 O(Fragment=2) 0.020930 1.999897 -0.000928 O(Fragment=3) -1.766147 0.018925 0.938278 O(Fragment=4) -0.938235 0.009006 -1.766248 O(Fragment=5) 0.938236 -0.008993 1.766248 O(Fragment=6) 1.766148 -0.018912 -0.938278 O(Fragment=7) -0.020929 -1.999884 0.000928 H(Fragment=2) -0.508951 2.591673 -0.557495 H(Fragment=2) 0.562411 2.580882 0.555837 H(Fragment=3) -2.253533 0.798638 1.248259 H(Fragment=3) -2.270468 -0.750283 1.247407 H(Fragment=4) -0.542006 0.006388 -2.651473 H(Fragment=4) -1.898222 0.017369 -1.902694 H(Fragment=5) 1.898228 -0.016775 1.902692 H(Fragment=5) 0.542004 -0.007343 2.651475 H(Fragment=6) 2.270516 0.750215 -1.247533 H(Fragment=6) 2.253469 -0.798707 -1.248151 H(Fragment=7) -0.562448 -2.580867 -0.555812 H(Fragment=7) 0.508968 -2.591675 0.557476 Fe 0 aug-cc-pVTZ **** H O 0 aug-cc-pVDZ **** ------------------------- Can someone please let me know how to get around this? Thanks so much! - Pratima Satish. Email: ps544,+,cornell.edu From owner-chemistry@ccl.net Wed Jul 24 17:03:01 2013 From: "Fedor Goumans goumans^_^scm.com" To: CCL Subject: CCL:G: How to calculate the EDA using G09 mol files in ADF Message-Id: <-49013-130724115239-28316-er21KhxPt4ByONE83aa9bw]*[server.ccl.net> X-Original-From: Fedor Goumans Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 24 Jul 2013 17:51:28 +0200 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [goumans .. scm.com] Dear Ranjita Das, You can import your coordinates (and bond information) directly from a .mol file in ADFGUI. For an energy decomposition analysis calculation you need the first run the fragment calculations, so there is no need to import any wavefunction information for the whole system even if you could. To get started with EDA, perhaps you find this teaching exercise helpful: http://www.scm.com/Doc/Teaching/MSc/page5.html Let us know at support[*]scm.com if you have any further questions or problems. Best wishes, Fedor On 7/24/2013 3:53 PM, ranjita das ranjitadas.85(!)gmail.com wrote: > Hi everybody, > I am recently using ADF package. for my systems, I have optimized them > with G09 package. Now I want to carry out energy decomposition > analysis using ADF. > Now I want to now, if it is possible to perform this analysis with ADF > importion the coordinates of the system from the Gaussian09 generated > mol files (mol files of the G09 optimized structures), since G09 uses > GTO whereas ADF uses STO. > Thanks > > > -- Dr. T. P. M. (Fedor) Goumans Business Developer Scientific Computing & Modelling NV (SCM) Vrije Universiteit, FEW, Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam, The Netherlands T +31 20 598 7625 F +31 20 598 7629 E-mail: goumans[*]scm.com http://www.scm.com From owner-chemistry@ccl.net Wed Jul 24 17:38:00 2013 From: "Jim Kress ccl_nospam- -kressworks.com" To: CCL Subject: CCL:G: What settings should I use in G09W to prevent the breaking of a bond? Message-Id: <-49014-130724134457-5156-i6hblAIUo/8LHVSr8Jwh5Q#%#server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Type: multipart/related; boundary="----=_NextPart_000_00D8_01CE8874.01008C00" Date: Wed, 24 Jul 2013 13:45:01 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam=kressworks.com] This is a multipart message in MIME format. ------=_NextPart_000_00D8_01CE8874.01008C00 Content-Type: multipart/alternative; boundary="----=_NextPart_001_00D9_01CE8874.01008C00" ------=_NextPart_001_00D9_01CE8874.01008C00 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Gabriela, Any particular reason you chose the deprotonated version of Cysteine? This is the usual form: http://en.wikipedia.org/wiki/Cysteine Jim > From: owner-chemistry+ccl_nospam==kressworks.com#,#ccl.net [mailto:owner-chemistry+ccl_nospam==kressworks.com#,#ccl.net] On Behalf Of kalyan onekalyan^-^yahoo.com Sent: Tuesday, July 23, 2013 3:15 PM To: Kress, Jim Subject: CCL:G: What settings should I use in G09W to prevent the breaking of a bond? Just use b3lyp/6-311+g(d,p) nosym opt freq pop=full gfprint . Hope it work. Best Regards Kalyan _____ > From: Dr. Vitaly Chaban vvchaban__gmail.com Sent: 23/07/2013 21:06 To: Dhar, Kalyan kumar Subject: CCL:G: What settings should I use in G09W to prevent the breaking of a bond? If bonds breaks, this means that your method is not perfect for your task. My first step would be to change the method / increase basis set. If B3LYP cannot predict right geometry, how can you be sure that it produces right frequencies and orbital energies? Gaussian can impose certain constraints during optimization, see "freeze" in the manual: http://www.gaussian.com/g_tech/g_ur/k_opt.htm Good luck! Dr. Vitaly V. Chaban On Tue, Jul 23, 2013 at 2:02 AM, Gabriela Arias gabriela.ariasdelarosa ~~ gmail.com < owner-chemistry ~ ccl.net> wrote: Sent to CCL by: "Gabriela Arias" [gabriela.ariasdelarosa[-] gmail.com] Hello everyone: I am doing an optimization and frequency calculation in Gaussian09 to obtain the Raman and Infrared spectra of cysteine. In the output, the bond between the thiol group and the adjacent carbon is broken, which is wrong. What can I do to prevent this bond from breaking? These are the settings that I am using: %nprocshared=2 # opt=tight freq=raman b3lyp/6-311+g geom=connectivity Title Card Required -1 1 C -2.18907515 2.08528252 -2.35362466 C -2.51526953 1.22134909 -1.12122202 O -2.82257852 1.77040643 -0.03142030 N -0.74900832 2.37936285 -2.37861038 H -0.23470752 1.52307575 -2.42622442 H -0.53719378 2.94035858 -3.17887183 O -2.46894955 -0.20480359 -1.21525919 C -2.57949898 1.32244966 -3.63317742 H -2.02919712 0.40622247 -3.68412445 H -2.35285743 1.92271509 -4.48945717 H -2.73937700 3.00150971 -2.30267762 C -4.08814042 1.01436550 -3.60700190 H -4.35940892 0.48434527 -4.49604181 H -4.63844227 1.93059270 -3.55605487 S -4.46517029 0.01579310 -2.18253651 H -5.74849515 -0.24627848 -2.16027033 1 2 1.0 4 1.0 8 1.0 11 1.0 2 3 2.0 7 1.0 3 4 5 1.0 6 1.0 5 6 7 8 9 1.0 10 1.0 12 1.0 9 10 11 12 13 1.0 14 1.0 15 1.0 13 Best regards and thanks for your help, Gabriela
CHEMISTRY ~ ccl.net or use: CHEMISTRY-REQUEST ~ ccl.net or use http://www.ccl.net Job: http://www.ccl.net/jobs Conferences: http://server.ccl.net/chemistry/announcements/conferences/ Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
http://www.ccl.net/chemistry/aboutccl/instructions/

Gabriela,

 

Any particular = reason you chose the deprotonated version of Cysteine?  This is the usual form:

3DCysteine


http://en.wikipedia.org/wiki/Cysteine

 

Jim

 

From: = owner-chemistry+ccl_nospam=3D=3Dkressworks.com#,#ccl.net = [mailto:owner-chemistry+ccl_nospam=3D=3Dkressworks.com#,#ccl.net] On = Behalf Of kalyan onekalyan^-^yahoo.com
Sent: Tuesday, July = 23, 2013 3:15 PM
To: Kress, Jim
Subject: = CCL:G: What settings should I use in G09W to prevent the breaking of a = bond?

 

Just use b3lyp/6-311+g(d,p) nosym opt = freq pop=3Dfull gfprint .
Hope it work.

Best Regards =
Kalyan

From: Dr. Vitaly Chaban = vvchaban__gmail.com
Sent: 23/07/2013 21:06
To: Dhar, Kalyan kumar
Subject: CCL:G: What settings should I use in G09W = to prevent the breaking of a bond?

If bonds breaks, = this means that your method is not perfect for your task. My first step = would be to change the method / increase basis set. If B3LYP cannot = predict right geometry, how can you be sure that it produces right = frequencies and orbital energies?

 

Gaussian can impose = certain constraints during optimization, see "freeze" in the = manual: http://www.gaussian.com/g_tech/g_ur/k_opt.htm

 

Good = luck!


<= div>

Dr. Vitaly V. = Chaban

 

 

 

 

 

On Tue, Jul 23, 2013 = at 2:02 AM, Gabriela Arias gabriela.ariasdelarosa ~~ gmail.com = <owner-chemistry ~ = ccl.net> = wrote:


Sent to CCL by: = "Gabriela  Arias" = [gabriela.ariasdelarosa[-]gmail.com]
Hello = everyone:

I am doing an optimization and frequency calculation in = Gaussian09 to obtain the Raman and Infrared spectra of cysteine. In the = output, the bond between the thiol group and the adjacent carbon is = broken, which is wrong. What can I do to prevent this bond from = breaking? These are the settings that I am = using:

%nprocshared=3D2
# opt=3Dtight freq=3Draman = b3lyp/6-311+g geom=3Dconnectivity

Title Card Required

-1 = 1
 C                 = -2.18907515    2.08528252   -2.35362466
 C   =               -2.51526953   =  1.22134909   -1.12122202
 O       =           -2.82257852    1.77040643 =   -0.03142030
 N             =     -0.74900832    2.37936285   = -2.37861038
 H               =   -0.23470752    1.52307575   -2.42622442
 H =                 -0.53719378 =    2.94035858   -3.17887183
 O     =             -2.46894955   -0.20480359 =   -1.21525919
 C             =     -2.57949898    1.32244966   = -3.63317742
 H               =   -2.02919712    0.40622247   -3.68412445
 H =                 -2.35285743 =    1.92271509   -4.48945717
 H     =             -2.73937700   =  3.00150971   -2.30267762
 C       =           -4.08814042    1.01436550 =   -3.60700190
 H             =     -4.35940892    0.48434527   = -4.49604181
 H               =   -4.63844227    1.93059270   -3.55605487
 S =                 -4.46517029 =    0.01579310   -2.18253651
 H     =             -5.74849515   -0.24627848 =   -2.16027033

 1 2 1.0 4 1.0 8 1.0 11 1.0
 2 3 = 2.0 7 1.0
 3
 4 5 1.0 6 = 1.0
 5
 6
 7
 8 9 1.0 10 1.0 12 = 1.0
 9
 10
 11
 12 13 1.0 14 1.0 15 = 1.0
 13

Best regards and thanks for your = help,

Gabriela



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We are happy to announce that Stefano Forli and Michel Sanner, both lead developers at the Molecular Graphics Lab at The Scripps Institute, La Jolla, California, offer a week of their time to present overviews and interna of AutoDock and the MGLtools for in silico drug screening and protein visualisation.They will introduce participants to their workflows comprising the whole process * from ligand preparation * via job control for high throughput docking * to result evaluation. The workshop offers lectures and exercises to support the participants in gaining experience and improving their skills in the above described tasks. Participants are encouraged to bring their own data for a fruitful exchange among themselves and the developers. For more details please visit http://www.gradschool.uni-luebeck.de/autodock Hoping to welcome many of you in September in Lbeck. We would appreciate if you disseminated this workshop announcement among potentially interested colleagues! With kind regards Steffen Mller, Department of Dermatology, University of Lbeck Katja Dau, Graduate Scool for Computing in Medicine and Life Sciences, University of Lbeck From owner-chemistry@ccl.net Wed Jul 24 18:48:01 2013 From: "kalyan onekalyan(~)yahoo.com" To: CCL Subject: CCL: Fw: PCM and di-electric constant 12 Message-Id: <-49016-130724153836-4623-x79Shsx3s/vXY0mgLfzaIQ,+,server.ccl.net> X-Original-From: kalyan Content-Type: multipart/alternative; boundary="1679980782-519141996-1374694711=:4965" Date: Wed, 24 Jul 2013 12:38:31 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: kalyan [onekalyan=yahoo.com] --1679980782-519141996-1374694711=:4965 Content-Type: text/plain; charset=us-ascii ----- Forwarded Message ----- >From: kalyan >To: CCL Subscribers >Sent: Wednesday, July 24, 2013 8:36 PM >Subject: PCM and di-electric constant 12 > > > >Can someone helping me how I will run my calc with sp. di- electric const 12 in PCM calculations.(implicit solvation method) and RTIL > >Best Regards >Kalyan > > > --1679980782-519141996-1374694711=:4965 Content-Type: text/html; charset=us-ascii

----- Forwarded Message -----
From: kalyan <onekalyan[*]yahoo.com>
To: CCL Subscribers <chemistry[*]ccl.net>
Sent: Wednesday, July 24, 2013 8:36 PM
Subject: PCM and di-electric constant 12

Can someone helping me how I will run my calc with sp. di- electric const 12 in PCM calculations.(implicit solvation method) and RTIL

Best Regards
Kalyan


--1679980782-519141996-1374694711=:4965--