From owner-chemistry@ccl.net Fri Sep 10 07:50:00 2010 From: "jaleel uc jaleel.uc]^[gmail.com" To: CCL Subject: CCL: : open+ parellel docking software Message-Id: <-42722-100910072956-16109-QtKyvBRBcANIkg63+rkrjA\a/server.ccl.net> X-Original-From: jaleel uc Content-Type: multipart/alternative; boundary=000325575efe85cf9f048fe61096 Date: Fri, 10 Sep 2010 16:59:49 +0530 MIME-Version: 1.0 Sent to CCL by: jaleel uc [jaleel.uc/./gmail.com] --000325575efe85cf9f048fe61096 Content-Type: text/plain; charset=ISO-8859-1 > Dear all > > Please suggest me a soft ware for docking (parallel and open source ) > > Can I use auto dock for the same ? > > Can I use NAMD directly for docking . ? > > with regards > > > Dr U.C.A.Jaleel. > Asst Professor in cheminformatics > Cheminformatics Division( UGC) > Malabar Christian College > Calicut University > -- Dr U.C.A.Jaleel. Asst Professor in cheminformatics Cheminformatics Division( UGC) Malabar Christian College Calicut University --000325575efe85cf9f048fe61096 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Dear=A0 all
=A0
=A0=A0=A0= Please suggest me a soft ware for=A0 docking=A0 (parallel and open source = )
=A0=A0
=A0=A0=A0 Can I use auto dock=A0 for the same ?
=A0=A0
=A0=A0=A0 Can=A0 I use NAMD=A0 directly for docking . ?
=A0=A0 with regards=A0
=A0

Dr U.C.A.Jaleel.
Asst Professor in c= heminformatics
Cheminformatics Division( UGC)
Malabar Christian Coll= ege
Calicut University



--
Dr U.C.A.Jaleel.
Ass= t Professor in cheminformatics
Cheminformatics Division( UGC)
Malaba= r Christian College
Calicut University
--000325575efe85cf9f048fe61096-- From owner-chemistry@ccl.net Fri Sep 10 08:55:01 2010 From: "errol lewars elewars_+_trentu.ca" To: CCL Subject: CCL: DFT maths Message-Id: <-42723-100910084644-14662-bFLYceU1kZeMs5aVxb2XOA*o*server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 10 Sep 2010 08:47:08 -0400 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars() trentu.ca] 2010 Sept 10 For the real stuff (mathematics) of DFT read _Density Functional Theory of Atoms and Molecules_, R. G. Parr, W. Yang, Oxford University Press, 1989. E. Lewars == neeraj m neerajmisra..hotmail.com wrote: > Sent to CCL by: "neeraj m" [neerajmisra]_[hotmail.com] > I shall very appreciate if any of you all could suggest me the real stuff(mathematics) of Density functional theory.Where can i get the complete....> > > From owner-chemistry@ccl.net Fri Sep 10 09:51:00 2010 From: "Toomas Tamm tt-ccl2(0)yki.ttu.ee" To: CCL Subject: CCL: Gsolv - pKa - Frequency Message-Id: <-42724-100910060159-6645-Cm8e+CG48w7nrJaEuJP3jg-*-server.ccl.net> X-Original-From: Toomas Tamm Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 10 Sep 2010 13:01:47 +0300 Mime-Version: 1.0 Sent to CCL by: Toomas Tamm [tt-ccl2,,yki.ttu.ee] On Sun, 2010-09-05 at 10:45 -0500, Christopher Cramer cramer..umn.edu wrote: > At that point, the "best" (in my opinion) way to define the free > energy in solution is to do a continuum calculation and add the > derived free energy of solvation to the gas phase free energy. I have been using this (or similar) schemes and trying to very briefly justify them in the resulting papers. This has led to questions from reviewers about the approximations, and I have had no better place to refer them to than the CCL archives. Is there a research paper (or book) which could be referenced which would explain and justify this way of calculating free energies in solution? If there is none, here is a suggestion to someone authoritative (Chris, Andreas, ...) to write one. -- Toomas Tamm e-mail: tt-ccl2 (at) kky . ttu . ee Chair of Inorganic Chemistry voice: INT+372-620-2810 Tallinn University of Technology fax: INT+372-620-2828 Ehitajate tee 5, EE-19086 Tallinn, Estonia http://www.kk.ttu.ee/toomas/ From owner-chemistry@ccl.net Fri Sep 10 11:08:00 2010 From: "vadiraj kurdekar vadirajgcppc,+,yahoo.co.in" To: CCL Subject: CCL: : open+ parellel docking software Message-Id: <-42725-100910093013-24688-UGDCcJVilowrepIFmAWPkQ(0)server.ccl.net> X-Original-From: vadiraj kurdekar Content-Type: multipart/alternative; boundary="0-306535658-1284125397=:97698" Date: Fri, 10 Sep 2010 18:59:57 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: vadiraj kurdekar [vadirajgcppc%yahoo.co.in] --0-306535658-1284125397=:97698 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable hello sir =A0 you can use DOVIS 2.0=A0 an efficient and easy to use parallel virtual scre= ening tool based on AutoDock 4.0 works only on linux which is available fre= ely for academic purpose. it have option of distrubuting work over clusters= and you can resume from that point where process was terminated. you can g= et imore nformation in this article Chemistry Central Journal 2008, 2:18=A0=A0 doi:10.1186/1752-153X-2-18 http://www.journal.chemistrycentral.com/content/2/1/18 =A0 if you are working on windows use autodock vina a open-source program for d= rug discovery. in paramerer file mention no. of processor to be used as 1 i= f your system is single core (pentium 4 and early), 2 if your system is dua= l core (AMD 64, or intel core 2 duo), 4 if your system is quad core=20 =A0 With Regards, =A0 Vadiraj Kurdekar, Research Scholar,=20 Pharmacy group, Birla Institute of Technology and Science-Pilani, Rajasthan, India. This e-mail (and any attachments), is confidential and may be privileged. I= t may be read, copied and used only by intended recipients. Unauthorized ac= cess to this e-mail (or attachments) and disclosure or copying of its conte= nts or any action taken in reliance on it is unlawful. Unintended recipient= s must notify the sender immediately by e-mail/phone & delete it from their= system without making any copies or disclosing it to a third person. --- On Fri, 10/9/10, jaleel uc jaleel.uc]^[gmail.com wrote: > From: jaleel uc jaleel.uc]^[gmail.com Subject: CCL: : open+ parellel docking software To: "Kurdekar, Vadiraj " Date: Friday, 10 September, 2010, 4:59 PM Dear=A0 all=20 =A0 =A0=A0=A0 Please suggest me a soft ware for=A0 docking=A0 (parallel and ope= n source ) =A0=A0=20 =A0=A0=A0 Can I use auto dock=A0 for the same ?=20 =A0=A0=20 =A0=A0=A0 Can=A0 I use NAMD=A0 directly for docking . ? =A0 =A0 with regards=A0 =A0 Dr U.C.A.Jaleel. Asst Professor in cheminformatics=20 Cheminformatics Division( UGC) Malabar Christian College=20 Calicut University --=20 Dr U.C.A.Jaleel. Asst Professor in cheminformatics=20 Cheminformatics Division( UGC) Malabar Christian College=20 Calicut University =0A=0A --0-306535658-1284125397=:97698 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
hello sir
 
you can use DOVIS 2.0  an efficient and easy to use parallel virt= ual screening tool based on AutoDock 4.0 works only on linux which is avail= able freely for academic purpose. it have option of distrubuting work over = clusters and you can resume from that point where process was terminated. y= ou can get imore nformation in this article
Chemistry Central Journal 2008, 2:18   doi:10.1186/1752-153X-2-18
 
if you are working on windows use autodock vina a open-source program = for drug discovery. in paramerer file mention no. of processor to be used a= s 1 if your system is single core (pentium 4 and early), 2 if your system i= s dual core (AMD 64, or intel core 2 duo), 4 if your system is quad core
 
With Regards,
 
Vadiraj Kurdekar,
R= esearch Scholar,
P= harmacy group,
R= ajasthan,
I= ndia.

This e-mail = (and any attachments), is confidential and may be privileged. It may be rea= d, copied and used only by intended recipients. Unauthorized access to this= e-mail (or attachments) and disclosure or copying of its contents or any a= ction taken in reliance on it is unlawful. Unintended recipients must notif= y the sender immediately by e-mail/phone & delete it from their system = without making any copies or disclosing it to a third person.

<= FONT style=3D"FONT-FAMILY: garamond, new york, times, serif" size=3D3 face= =3D"verdana, helvetica, sans-serif">


--- On = Fri, 10/9/10, jaleel uc jaleel.uc]^[gmail.com <owner-chemistry.:.ccl= .net> wrote:

From: jaleel uc jaleel.uc]^[gmail.com <owner-c= hemistry.:.ccl.net>
Subject: CCL: : open+ parellel docking software
= To: "Kurdekar, Vadiraj " <vadirajgcppc.:.yahoo.co.in>
Date: = Friday, 10 September, 2010, 4:59 PM


Dear  all
&nb= sp;
    Please suggest me a soft ware for  docking&n= bsp; (parallel and open source )
  
    Can= I use auto dock  for the same ?
  
  &nbs= p; Can  I use NAMD  directly for docking . ?
 
  = with regards 
 

Dr U.C.A.Jaleel.
Asst Professor in c= heminformatics
Cheminformatics Division( UGC)
Malabar Christian Coll= ege
Calicut University



--=
Dr U.C.A.Jaleel.
Asst Professor in cheminformatics
Cheminformat= ics Division( UGC)
Malabar Christian College
Calicut University
<= /DIV>

--0-306535658-1284125397=:97698-- From owner-chemistry@ccl.net Fri Sep 10 11:42:00 2010 From: "Frank Neese neese|,|thch.uni-bonn.de" To: CCL Subject: CCL: DFT maths Message-Id: <-42726-100910111352-25927-Jw17QOU1RiSfNmdS5aG23w*_*server.ccl.net> X-Original-From: Frank Neese Content-Type: multipart/alternative; boundary=Apple-Mail-5-881727656 Date: Fri, 10 Sep 2010 17:13:25 +0200 Mime-Version: 1.0 (Apple Message framework v1081) Sent to CCL by: Frank Neese [neese^^thch.uni-bonn.de] --Apple-Mail-5-881727656 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Dear Neeraj, I agree of couse with the previous suggestions. In addition, you may = also be interested to read:=20 Prediction of Molecular Spectra and Molecular Properties with Density = Functional Theory: from Fundamental Theory to Exchange Coupling. Coord. = Chem. Rev., 2009, 253, 526-563 which is elementary but specific. best regards, FN --Apple-Mail-5-881727656 Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=us-ascii Dear Neeraj,

I agree of couse with the previous suggestions. In addition, you may also be interested to read: 

Prediction of Molecular Spectra and Molecular Properties with Density Functional Theory: from Fundamental Theory to Exchange Coupling. Coord. Chem. Rev., 2009,  253, 526-563

which is elementary but specific.

best regards,
FN

--Apple-Mail-5-881727656-- From owner-chemistry@ccl.net Fri Sep 10 14:55:00 2010 From: "David Close closed*_*etsu.edu" To: CCL Subject: CCL:G: formchk of .chk file Message-Id: <-42727-100910145340-20028-4X4PxMtV4LHfK0NH/45eaA~~server.ccl.net> X-Original-From: "David Close" Date: Fri, 10 Sep 2010 14:53:38 -0400 Sent to CCL by: "David Close" [closed__etsu.edu] I have finished a normal Gaussian calculation and have information in a .chk file I would like to use. The Gaussian utility Formchk does not read the .chk file. Instead I get a segmentation error. Also I can not read the .chk file in GaussView. Does anyone know what to do to generate a usable .chk file? From owner-chemistry@ccl.net Fri Sep 10 15:31:00 2010 From: "Yi (Yves) Wang yves.wang\a/duke.edu" To: CCL Subject: CCL:G: formchk of .chk file Message-Id: <-42728-100910152228-28024-Y43T7QKpP4tzckOQKIuedQ(-)server.ccl.net> X-Original-From: "Yi (Yves) Wang" Content-Type: multipart/alternative; boundary=Apple-Mail-3-896657135 Date: Fri, 10 Sep 2010 15:22:15 -0400 Mime-Version: 1.0 (Apple Message framework v1081) Sent to CCL by: "Yi (Yves) Wang" [yves.wang*duke.edu] --Apple-Mail-3-896657135 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=GB2312 Hi David, Please make sure your formchk and Gaussian have the same architecture, = ie. they're all 32bit or 64bit. Best, = __________________________________________________________________________= ___ Yi (Yves) Wang Department of Biochemistry Structural Biology & Biophysics Program Duke University BS: University of Science and Technology of China School of Life Sciences, National Laboratory for Physical Sciences at = Microscale Tel: +1-919-236-3307 (Cell) +1-919-684-0235 (Lab 1) +1-919-660-1634 (Lab 2) Office: A20 LSRC / 5301 FFSC E-Mail: yves.wang|a|duke.edu Mail: Box 90317, Chemistry Department =D4=DA 2010-9-10=A3=AC=CF=C2=CE=E72:53=A3=AC David Close = closed*_*etsu.edu =D0=B4=B5=C0=A3=BA >=20 > Sent to CCL by: "David Close" [closed__etsu.edu] > I have finished a normal Gaussian calculation and have information in = a .chk file I would like to use. The Gaussian utility Formchk does not = read the .chk file. Instead I get a segmentation error. Also I can not = read the .chk file in GaussView. Does anyone know what to do to = generate a usable .chk file? >=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 --Apple-Mail-3-896657135 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=GB2312 Hi = David,

Please make sure your formchk and Gaussian = have the same architecture, ie. they're all 32bit or = 64bit.

Best,


Yi (Yves) Wang
Department of Biochemistry
Structural Biology & Biophysics = Program
Duke = University
BS: University = of Science and Technology of China
   +1-919-660-1634 (Lab 2)
Office: A20 LSRC / 5301 = FFSC
Mail: Box 90317, Chemistry = Department

=D4=DA 2010-9-10=A3=AC=CF=C2=CE=E72:53=A3=AC David Close = closed*_*etsu.edu =D0=B4=B5=C0=A3=BA


Sent to CCL by: "David  Close" = [closed__etsu.edu]
 I have finished a normal Gaussian = calculation and have information in a .chk file I would like to use. =  The Gaussian utility Formchk does not read the .chk file. Instead = I get a segmentation error.  Also I can not read the .chk file in = GaussView.  Does anyone know what to do to generate a usable .chk = file?



-=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
the strange characters on the top line to = the |a| sign. You can also
look up the X-Original-From: line in the = mail header.

E-mail to subscribers: CHEMISTRY|a|ccl.net or use:
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Before posting, check wait time at: = http://www.ccl.net

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If your mail bounces = > from CCL with 5.7.1 error, check:
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RTFI: http://www.cc= l.net/chemistry/aboutccl/instructions/


<= /div>
= --Apple-Mail-3-896657135-- From owner-chemistry@ccl.net Fri Sep 10 16:05:00 2010 From: "Jamin Krinsky jamink!=!berkeley.edu" To: CCL Subject: CCL:G: Potential energy scans on Gaussian - Possible From Initial Geometry? Message-Id: <-42729-100910150231-31655-h65nYlogQQrtNsJG9qauQg%a%server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 10 Sep 2010 12:02:23 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink|*|berkeley.edu] Hi Jeffrey, Hi haven't had a chance to look at these posts for a while but I just did and it doesn't look like your question has been answered. I've noticed too that relaxed scans in Gaussian tend to be path dependent, which is somewhat annoying. There is no way to automatically do what you are proposing, you would just have to set the appropriate dihedral and do a constrained minimization at each value of that dihedral. Or you could do that for a few points along the scan, and then do real scans between those points... Regards, Jamin On Fri, Sep 3, 2010 at 7:29 PM, Jeffrey Mo jdmo . mit.edu wrote: > > Sent to CCL by: "Jeffrey  Mo" [jdmo]=[mit.edu] > Hi everyone, > >  My first post!  Hopefully I'll get some help from you guys and be able to give some help in the future too. > >  I'm trying to perform a potential energy scan (PES) on short-chain alkyl/alkenyl radical transition states right now, and am running into a problem.  Gaussian starts each new optimization in the scan from the previous geometry; therefore, when I get all the way around (360 degrees) a dihedral, for instance, I often don't end up at the same geometry. > >  Is there a way that I can ask Gaussian to perform each new optimization from the initial geometry?  That is, let's say we're on scan job #19 of a 36-point dihedral scan (where each scan increments by 10 degrees) -- then, I just want to change the relevant dihedral by 180 degrees from the initial geometry, not by 10 degrees from the geometry of scan job #18.  Thanks in advance! > > Jeffrey Mo > MIT Chemical Engineering > Doctoral Candidate > jdmo-x-mit.edu>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > -- Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink%%berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu From owner-chemistry@ccl.net Fri Sep 10 16:40:00 2010 From: "Jamin Krinsky jamink---berkeley.edu" To: CCL Subject: CCL:G: formchk of .chk file Message-Id: <-42730-100910160127-5119-Xon7r69pDpi2ERfdZnr/yg__server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 10 Sep 2010 13:01:20 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink*berkeley.edu] Hi David, Was the Gaussian calculation run on the same computer system (same OS and version of Gaussian) as where you are using the formchk utility? This must be the case or the version of formchk will not be able to read the binary chk file. If this is not the problem, it may be that the default amount of memory used by formchk is not enough, in which case you can set that environment variable (something like setenv GAUSS_MEM "amount of memory you can use in words" in a linux c shell, check the Gaussian manual for specifics) before executing the formchk command. Regards, Jamin On Fri, Sep 10, 2010 at 11:53 AM, David Close closed*_*etsu.edu wrote: > > Sent to CCL by: "David  Close" [closed__etsu.edu] >  I have finished a normal Gaussian calculation and have information in a .chk file I would like to use.  The Gaussian utility Formchk does not read the .chk file. Instead I get a segmentation error.  Also I can not read the .chk file in GaussView.  Does anyone know what to do to generate a usable .chk file?>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > -- Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink|-|berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu From owner-chemistry@ccl.net Fri Sep 10 17:16:00 2010 From: "Eustis Soren soren.eustis[a]env.ethz.ch" To: CCL Subject: CCL:G: formchk of .chk file Message-Id: <-42731-100910161744-3639-CdhhrkCwzeqZgrFqLyiwUQ*|*server.ccl.net> X-Original-From: "Eustis Soren" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 10 Sep 2010 22:17:33 +0200 MIME-Version: 1.0 Sent to CCL by: "Eustis Soren" [soren.eustis-.-env.ethz.ch] David, I have found that when I run a calculation on some machines, I need to run formchk on that very machine in order to get a valid .fch file. This happens with transferring from 64 to 34 bit CPUs for sure. Soren On Sep 10, 2010, at 20:53, "David Close closed*_*etsu.edu" wrote: > > Sent to CCL by: "David Close" [closed__etsu.edu] > I have finished a normal Gaussian calculation and have information in a .chk file I would like to use. The Gaussian utility Formchk does not read the .chk file. Instead I get a segmentation error. Also I can not read the .chk file in GaussView. Does anyone know what to do to generate a usable .chk file?> > From owner-chemistry@ccl.net Fri Sep 10 17:51:01 2010 From: "David Hose Anthrax_brothers^^hotmail.com" To: CCL Subject: CCL:G: formchk of .chk file Message-Id: <-42732-100910162904-15482-KSvuA2Sy/W+X/LkBREO++g _ server.ccl.net> X-Original-From: "David Hose" Date: Fri, 10 Sep 2010 16:29:03 -0400 Sent to CCL by: "David Hose" [Anthrax_brothers(a)hotmail.com] David, A quick look through the CCL archives suggests that you should convert the .chk to the .fchk on the same machine that created the .chk file. http://www.ccl.net/chemistry/resources/messages/2008/04/03.003-dir/index.html http://www.ccl.net/cgi-bin/ccl/message-new?2008+04+06+005 http://www.ccl.net/chemistry/resources/messages/2005/06/13.003-dir/index.html Hope these posts can help you sort out your problem. Regards, Dave. ============== Sent to CCL by: "David Close" [closed__etsu.edu] I have finished a normal Gaussian calculation and have information in a .chk file I would like to use. The Gaussian utility Formchk does not read the .chk file. Instead I get a segmentation error. Also I can not read the .chk file in GaussView. Does anyone know what to do to generate a usable .chk file? From owner-chemistry@ccl.net Fri Sep 10 18:34:00 2010 From: "errol lewars elewars#%#trentu.ca" To: CCL Subject: CCL: Absolute bascity in the gas phase Message-Id: <-42733-100910182914-18200-ZcdsQ4KBQdws4tc6NHn4Ng*server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 10 Sep 2010 18:29:25 -0400 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars()trentu.ca] 2010 Sept 10 Hello, For the entropy of the proton, see G J Tawa et al, J Chem Phys, 1998, 109(12), 4852-4863; also look up the Sackur-Tetrode equation (for the entropy of a particle in terms of pressure, temperature, and its mass). Enthalpy of the proton: E I von Nagy-Felsobuki, K Kimura, J Phys Chem, 1990, 94, 8041-8044. E. Lewars == Sayed Mesa elsayed.elmes|*|yahoo.com wrote: > Sent to CCL by: "Sayed Mesa" [elsayed.elmes]^[yahoo.com] > Thanks for the senders. Yes Jan, the link you sent seems better and useful (it is plentiful with data) because I already have this paper but without data involved in it. The conclusion is "The electronic energy of H+ = zero because it has not electron. The only non-zero energy term is the translational energy term which is equal to 3/2RT=0.889 Kcal/mol." > > I still have a question how you can calculate the entropy for H+ in the below reaction? > > B + H+ -----> BH > Thanks in advance > Sayed > > ---------------------------------- > Sent to CCL by: Jan Labanowski [janl!A!speakeasy.net] > Mahmoud A. A. Ibrahim m.ibrahim#,#compchem.net writes: > >> Dear SayedYou may like to have a look on the following paper >> ( http://www.ccl.net/cca/documents/proton-affinity/affinities.pdf, unpublished ) >> > The better link may be http://www.ccl.net/cca/documents/proton-affinity since it > will also provide the links to the tables for the paper (for what it is worth...). > Jan> > > From owner-chemistry@ccl.net Fri Sep 10 20:26:00 2010 From: "Haibin Scopus lihb734:_:yahoo.com" To: CCL Subject: CCL:G: Unable to restart since not pure spin-state Message-Id: <-42734-100910201151-27972-/wBuOQLm8k9jZPH8HyBrwQ**server.ccl.net> X-Original-From: Haibin Scopus Content-Type: multipart/alternative; boundary="0-522702226-1284163904=:31914" Date: Fri, 10 Sep 2010 17:11:44 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Haibin Scopus [lihb734/a\yahoo.com] --0-522702226-1284163904=:31914 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sir,=20 =A0=A0=A0 When I performed a TDDFT excited optimzation on a Mn(II) complex = using Gaussian09, the output has an error "Unable to restart since not pure= spin-state", what it means? How can I solve this problem?=20 =A0=A0 Any suggestion will be highly appreciated. Best wishes! =A0 PS: The routine=A0line in =A0my input file is, =A0#p BP86/gen td(triplets,nstates=3D12,Root=3D2) popt(maxcycle=3D512) gfin= put=A0=A0test =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0 =A0 Haibin Li Ph. D candidate Institute of Functional Material Chemistry, Faculty of Chemistry Northeast Normal University=20 changchun, Jilin, 130024 PR CHINA E-mail: lihb734^nenu.edu.cn; lihb734^yahoo.com http://www.nenu.edu.cn=0A=0A=0A --0-522702226-1284163904=:31914 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Sir,
    When I performed a TDDFT excited optimzation on a M= n(II) complex using Gaussian09, the output has an error "Unable to restart = since not pure spin-state", what it means? How can I solve this problem?
   Any suggestion will be highly appreciated. Best wishes!
 
PS: The routine line in  my input file is,
 #p BP86/gen td(triplets,nstates=3D12,Root=3D2) popt(maxcycle=3D5= 12) gfinput  test
           &nbs= p;            &= nbsp;           &nbs= p;            &= nbsp;           &nbs= p;            &= nbsp;      
 
Haibin Li Ph. D candidate
Institute of Functional Material Chemistry, Faculty of Chemistry
Northeast Normal University
changchun, Jilin, 130024 PR = CHINA

E-mail: lihb734^nenu.edu.cn; lihb734^yahoo.com
http://www.n= enu.edu.cn

=0A=0A --0-522702226-1284163904=:31914-- From owner-chemistry@ccl.net Fri Sep 10 21:00:01 2010 From: "Sayed Mesa elsayed.elmes.:.yahoo.com" To: CCL Subject: CCL: Enthalpy of proton Message-Id: <-42735-100910205821-8197-j8vfNZdFNQKVuSPJuCmdEw+*+server.ccl.net> X-Original-From: "Sayed Mesa" Date: Fri, 10 Sep 2010 20:58:20 -0400 Sent to CCL by: "Sayed Mesa" [elsayed.elmes]-[yahoo.com] Dear CCL community I am confused in the following point: The enthalpy of H+ ion in gas phase is 3/2RT or 5/2RT? The reference for 3/2RT is "exploring chemistry with electronic structure methods page 168" The reference for 5/2RT is "Calculation of the aqueous solvation free energy of the proton, J. Chem. Phys. Vol. 109 page 4852" Which one is correct? Thanks for your help Sayed From owner-chemistry@ccl.net Fri Sep 10 21:48:00 2010 From: "Chad Risko cmrisko*o*gmail.com" To: CCL Subject: CCL:G: TDDFT transition density Gaussian09 Message-Id: <-42736-100910162501-11117-GGW96qzPR/3pLcnlTOwrMg:_:server.ccl.net> X-Original-From: "Chad Risko" Date: Fri, 10 Sep 2010 16:25:00 -0400 Sent to CCL by: "Chad Risko" [cmrisko],[gmail.com] Dear CCLers, I am interested in plotting the transition density from TDDFT calculations in Gaussian09. Looking through the CCL archives, it appears that the method to do this changed at some point, and I wonder if anyone has any quick instructions/examples on the necessary keywords. Thanks so much in advance! Best regards, Chad