From owner-chemistry@ccl.net Fri Jun 25 00:06:00 2010 From: "zineb el adnani zinebeladnani(~)hotmail.com" To: CCL Subject: CCL: restart calculation Gaussian FREQ / OPT chk file Message-Id: <-42179-100624210344-21966-t5bixxkhwEOxsyX1SSGvJg _ server.ccl.net> X-Original-From: zineb el adnani Content-Type: multipart/alternative; boundary="_f117edc7-98c4-4a47-a0e9-dea8b5277b17_" Date: Fri, 25 Jun 2010 01:03:33 +0000 MIME-Version: 1.0 Sent to CCL by: zineb el adnani [zinebeladnani(-)hotmail.com] --_f117edc7-98c4-4a47-a0e9-dea8b5277b17_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi=2C I usually restart my job from the last geom calculated in my unfinished cal= cul and I use guess=3Dread with the same route section as before (you will = have to keep the same chk file name)=2C I hope it help=3B regards Zineb EL ADNANI =20 _________________________________________________________________ Hotmail : un service de messagerie gratuit=2C fiable et complet https://signup.live.com/signup.aspx?id=3D60969= --_f117edc7-98c4-4a47-a0e9-dea8b5277b17_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi=2C
I usually restart my job from the last geom calculated in my unfin= ished calcul and I use guess=3Dread with the same route section as before (= you will have to keep the same chk file name)=2C I hope it help=3B

r= egards
Zineb EL ADNANI

Hotmail : un service d= e messagerie gratuit=2C fiable et complet Profitez-en = --_f117edc7-98c4-4a47-a0e9-dea8b5277b17_-- From owner-chemistry@ccl.net Fri Jun 25 01:21:00 2010 From: "Thishana Singh singht^-^dut.ac.za" To: CCL Subject: CCL:G: Gaussian upgrade Message-Id: <-42180-100625011909-20999-O94Snn+rO+ShSnqXfe7hxQ~!~server.ccl.net> X-Original-From: "Thishana Singh" Date: Fri, 25 Jun 2010 01:19:07 -0400 Sent to CCL by: "Thishana Singh" [singht]~[dut.ac.za] Dear Serdar I had a problem viewing frequency output files in GV3 when I upgraded to G09. If your budget allows you to upgrade GaussView, I would suggest that you get the latest version of GaussView as well. I hope this helps. Thishana Singh Department of Chemistry Durban University of Technology Durban South Africa Sent to CCL by: "Serdar Badoglu" [sbadoglu%%gazi.edu.tr] Hi CCL'ers We use Gaussian 03W with GaussView 3. Nowadays we're thinking of upgrading ourself to Gaussian 09W Multiprocessor. I'd like to ask that if you know any compatibility issues between G09W and GV3. May we continue to use GV3 when we upgrade to G09W without problems? Or, should we upgrade also GaussView? Thanks. Serdar Badoglu Gazi University Dept. of Physics From owner-chemistry@ccl.net Fri Jun 25 02:15:00 2010 From: "rocky walden rocky.walden19(_)gmail.com" To: CCL Subject: CCL: Installation of TURBOMOLE on a Cluster with 24 Nodes... Message-Id: <-42181-100625020939-28627-tusaEzvh5DVxCl4xeLN2Qg~~server.ccl.net> X-Original-From: rocky walden Content-Type: multipart/alternative; boundary=90e6ba18187c753fce0489d49daa Date: Fri, 25 Jun 2010 11:39:34 +0530 MIME-Version: 1.0 Sent to CCL by: rocky walden [rocky.walden19**gmail.com] --90e6ba18187c753fce0489d49daa Content-Type: text/plain; charset=ISO-8859-1 Hi All, Thank you very much for you time. My professor has recently procured a HP-UX cluster with 24 nodes ( operating system is UNIX), he assigned the work to me. Now we are planning to instal Turbomole on it, I have gone throught the installation manual but i did not find any cluster installation information reported. I think some of you might have installed Turbomole on Cluster with edition in Bashrc file. Can you please pass me a detailed information how to install the turbomole application successfully with editing the Bashrc file. Looking forward to hear form you. Your help is much benificial to me a person who is not a Computer expert. Regards. Walden R --90e6ba18187c753fce0489d49daa Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi All,
=A0 Thank you very much for you time.
=A0 My professor has recently procured a HP-UX cluster with 24 nodes (= operating system is UNIX), he assigned the work to me.
=A0 Now we are planning to instal Turbomole on it, I have gone through= t the installation manual but=A0i did not find any cluster installation inf= ormation reported.
=A0 I think some of you might have installed Turbomole on Cluster with= edition in Bashrc file.
=A0 Can you please pass me a detailed information=A0how to install the= turbomole application successfully with editing the Bashrc file.
=A0
=A0
Looking forward to hear form you.
Your help is much benificial to me a person who is not a Computer expe= rt.
=A0
Regards.
Walden R
--90e6ba18187c753fce0489d49daa-- From owner-chemistry@ccl.net Fri Jun 25 03:23:00 2010 From: "Ulrike Salzner salzner:+:fen.bilkent.edu.tr" To: CCL Subject: CCL:G: Gaussian upgrade Message-Id: <-42182-100625024221-4060-ZbkFe/8ZcJbPugo9kFNaLg . server.ccl.net> X-Original-From: Ulrike Salzner Content-Type: multipart/alternative; boundary=00163649a339de3d670489d4bab3 Date: Fri, 25 Jun 2010 09:17:48 +0300 MIME-Version: 1.0 Sent to CCL by: Ulrike Salzner [salzner]=[fen.bilkent.edu.tr] --00163649a339de3d670489d4bab3 Content-Type: text/plain; charset=ISO-8859-1 Dear Serdar, some features work, some do not. You can see the geometry, but not frequencies and you can not plot orbitals. There might be more. For the frequencies somebody described a work around on CCL recently. Whether something can be done about the orbitals, I do not know. Why don't you ask Gaussian directly? Regards Ulrike On Thu, Jun 24, 2010 at 7:58 PM, Serdar Badoglu sbadoglu=gazi.edu.tr < owner-chemistry|-|ccl.net> wrote: > > Sent to CCL by: "Serdar Badoglu" [sbadoglu%%gazi.edu.tr] > Hi CCL'ers > > We use Gaussian 03W with GaussView 3. Nowadays we're thinking of upgrading > ourself to Gaussian 09W Multiprocessor. I'd like to ask that if you know any > compatibility issues between G09W and GV3. May we continue to use GV3 when > we upgrade to G09W without problems? Or, should we upgrade also GaussView? > > Thanks. > > > Serdar Badoglu > Gazi University > Dept. of Physics> > > -- Assoc. Prof. Ulrike Salzner Department of Chemistry Bilkent University 06800 Bilkent, Ankara --00163649a339de3d670489d4bab3 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Serdar,
some features work, some do not. You can see the geometry, = but not frequencies and you can not plot orbitals. There might be more. For= the frequencies somebody described a work around on CCL recently. Whether = something can be done about the orbitals, I do not know. Why don't you = ask Gaussian directly?
Regards Ulrike

On Thu, Jun 24, 2010 at 7:= 58 PM, Serdar Badoglu sbadoglu=3Dgazi.edu.tr= <owner= -chemistry|-|ccl.net> wrote:

Sent to CCL by: "Serdar =A0Badoglu" [sbadoglu%%gazi.edu.tr]
Hi CCL'ers

We use Gaussian 03W with GaussView 3. Nowadays we're thinking of upgrad= ing ourself to Gaussian 09W Multiprocessor. I'd like to ask that if you= know any compatibility issues between G09W and GV3. May we continue to use= GV3 when we upgrade to G09W without problems? Or, should we upgrade also G= aussView?

Thanks.


Serdar Badoglu
Gazi University
Dept. of Physics



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06800 Bilkent, Ank= ara
--00163649a339de3d670489d4bab3-- From owner-chemistry@ccl.net Fri Jun 25 04:14:00 2010 From: "Uwe Huniar huniar-,-cosmologic.de" To: CCL Subject: CCL: Installation of TURBOMOLE on a Cluster with 24 Nodes... Message-Id: <-42183-100625040939-16197-6iwh+f173ZkDPSgDAFHvvQ:_:server.ccl.net> X-Original-From: Uwe Huniar Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 25 Jun 2010 10:09:28 +0200 MIME-Version: 1.0 Sent to CCL by: Uwe Huniar [huniar{=}cosmologic.de] Dear Walden, chapter 3.2 of the Turbomole documentation (version 6.2) is about parallel calculations, including a. environment settings (chapter 3.2.1), everything you need to add to your .bashrc b. running jobs on a cluster using several nodes without a queuing system (also chapter 3.2.1, page 36) c. a sample PBS start script for submitting jobs to a queuing system If you have Turbomole and problems with installation, please just contact the Turbomole Support - that is what support is for... Someone at your institute must have installed the 24 node cluster and maintains it now - show him the chapter in the Turbomole manual I have mentioned, and if there are still open questions: Turbomole support. Note that except of installing the usual Turbomole distribution, nothing has to be installed in addition - MPI environment, runtime libraries, etc. are either all included (Linux) or the default tools are used (HP-UX, AIX, ...). So you do not have to care about which MPI to use, how to set it, and so on. Regards, Uwe Am 25.06.2010 08:09, schrieb rocky walden rocky.walden19(_)gmail.com: > Hi All, > Thank you very much for you time. > My professor has recently procured a HP-UX cluster with 24 nodes ( > operating system is UNIX), he assigned the work to me. > Now we are planning to instal Turbomole on it, I have gone throught the > installation manual but i did not find any cluster installation information > reported. > I think some of you might have installed Turbomole on Cluster with edition > in Bashrc file. > Can you please pass me a detailed information how to install the turbomole > application successfully with editing the Bashrc file. > > > Looking forward to hear form you. > Your help is much benificial to me a person who is not a Computer expert. > > Regards. > Walden R > -- ------------------------------------------------------------------------------ Dr. Uwe Huniar COSMOlogic GmbH & Co. KG From owner-chemistry@ccl.net Fri Jun 25 04:49:00 2010 From: "Isabelle Navizet navizet^-^univ-mlv.fr" To: CCL Subject: CCL:G: Gaussian upgrade Message-Id: <-42184-100625043259-20527-LIzQZ9gGjW5S0COJ3mSQJQ*o*server.ccl.net> X-Original-From: Isabelle Navizet Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="UTF-8" Date: Fri, 25 Jun 2010 16:33:06 +0800 Mime-Version: 1.0 Sent to CCL by: Isabelle Navizet [navizet===univ-mlv.fr] Hello Serdar and Ulrike, If you convert your g09 .chk to a .fchk file then you can see the orbitals in gview. It works for me. Isabelle On Fri, 2010-06-25 at 09:17 +0300, Ulrike Salzner salzner: +:fen.bilkent.edu.tr wrote: > Dear Serdar, > some features work, some do not. You can see the geometry, but not > frequencies and you can not plot orbitals. There might be more. For > the frequencies somebody described a work around on CCL recently. > Whether something can be done about the orbitals, I do not know. Why > don't you ask Gaussian directly? > Regards Ulrike > > On Thu, Jun 24, 2010 at 7:58 PM, Serdar Badoglu sbadoglu=gazi.edu.tr > wrote: > > Sent to CCL by: "Serdar Badoglu" [sbadoglu%%gazi.edu.tr] > Hi CCL'ers > > We use Gaussian 03W with GaussView 3. Nowadays we're thinking > of upgrading ourself to Gaussian 09W Multiprocessor. I'd like > to ask that if you know any compatibility issues between G09W > and GV3. May we continue to use GV3 when we upgrade to G09W > without problems? Or, should we upgrade also GaussView? > > Thanks. > > > Serdar Badoglu > Gazi University > Dept. of Physics > > > > -= This is automatically added to each message by the mailing > script =- > E-mail to subscribers: CHEMISTRY%%ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST%%ccl.net or use> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: > http://www.ccl.net/chemistry/searchccl/index.shtml> > > > > > -- > Assoc. Prof. Ulrike Salzner > Department of Chemistry > Bilkent University > 06800 Bilkent, Ankara -- ------------------------------------------------------------------------ Isabelle Navizet (Soury-Lavergne) 伊莎 add 1: Beijing Normal University, Department of Chemistry, room 517 add 2: Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallee, France equipe de Chimie Theorique de l'Universite de Marne la Vallee From owner-chemistry@ccl.net Fri Jun 25 05:24:00 2010 From: "Serdar Bado?lu sbadoglu ~~ gazi.edu.tr" To: CCL Subject: CCL: Gaussian upgrade Message-Id: <-42185-100625045409-15138-PtGqq847BwM8mvu7ADtchQ]=[server.ccl.net> X-Original-From: "Serdar Bado?lu" Date: Fri, 25 Jun 2010 08:53:53 -0000 Sent to CCL by: "Serdar Bado?lu" [sbadoglu ~ gazi.edu.tr] I always pay more attention to users' opinions. That's why I have asked this directly to CCL community first. Now I have two answers, and I have decided to what to do. Thank you all. Regards. -- Serdar BADOGLU Gazi University Department of Physics From owner-chemistry@ccl.net Fri Jun 25 06:47:00 2010 From: "Andrew Voronkov drugdesign-x-yandex.ru" To: CCL Subject: CCL: are there any good free 3D conformations generators? Message-Id: <-42186-100625064444-14003-sA5rEy3tm3NHcv2v4dP91g::server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 25 Jun 2010 14:44:36 +0400 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign[*]yandex.ru] Dear CCL users, can you please recommend the adequate free 3D generators like open source or generators which are free for all types of organizations? I have tried this software: http://users.abo.fi/mivainio/balloon/ but to say the truth quality is not very good (like corrupted aromaticity). Sincerely yours, Andrew From owner-chemistry@ccl.net Fri Jun 25 08:14:00 2010 From: "Jerome Kieffer jerome.Kieffer*_*terre-adelie.org" To: CCL Subject: CCL: Help needed in interpretation of NMR chemical sheilding values calculated using Computational Tool (TURBOMOLE) Message-Id: <-42187-100624162215-15954-lqcYtQU6pCDssK4bWuJCYQ]![server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 24 Jun 2010 22:22:05 +0200 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer**terre-adelie.org] On Thu, 24 Jun 2010 10:29:32 +0530 "rocky walden rocky.walden19~!~gmail.com" wrote: > Hi All, > I have recently downloaded the latest version of turbomole and started > working on it. > I used Hartree-Fock method i have optimized the geometry of the molecule > and next after optimization i have asked the application to Calculate NMR > chemical shielding values. > I job was success ful and i got a human readble file as an output, which > has the anisotropic and isotropic , values. > The values i got were different form the experimental. > My molecule is simple Acetaldehyde. > I cant find any value which is nearly matching to my experimental value. > > Is there any other calculation that i need to perform on my NMR chemical > shield out put values which simplifes and gives results in delta values ( > where experimental values are represented ). > > Looking forward for your help. REDO your calculation with TMS, take the difference, you should be close to the experiment for carbons (+- 2ppm). Hydrogens being on the outer layer of the molecule they are very much influenced by the solvent, so their error is usually close to 1 ppm (hence useable for prediction) Regards, -- Jérôme KIEFFER http://www.terre-adelie.org From owner-chemistry@ccl.net Fri Jun 25 08:49:00 2010 From: "Vladislav Vassiliev vladislav.vassiliev**anu.edu.au" To: CCL Subject: CCL: Creating publishable 2D drawings from 3D Z-matrix based input files Message-Id: <-42188-100625051754-11481-DyQ+qUXx9iTi2ZRjplx9hw]![server.ccl.net> X-Original-From: Vladislav Vassiliev Content-language: en Content-type: multipart/alternative; boundary="Boundary_(ID_+Izqm9tuI7kjujE94lnnCg)" Date: Fri, 25 Jun 2010 19:17:42 +1000 MIME-version: 1.0 Sent to CCL by: Vladislav Vassiliev [vladislav.vassiliev|*|anu.edu.au] This is a multi-part message in MIME format. --Boundary_(ID_+Izqm9tuI7kjujE94lnnCg) Content-type: text/plain; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Content-disposition: inline Hi John, Jamberoo, http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html, can read in several formats as Z-matrix. It can also produce 2D pictures as well as VRML files which, in turn, can be embedded into the pdf files (3d pdf). 3d pdf files can be read and visualized by the (freeware) Adobe Reader. Some publishers accept 3d pdf submissions. You can have a look at the sample 3d pdf files at the Jamberoo web pages. Regards, Vlad --Boundary_(ID_+Izqm9tuI7kjujE94lnnCg) Content-type: text/html; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Content-disposition: inline Hi John,

Jamberoo, http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html, can read in several formats as Z-matrix. It can also produce 2D pictures as well as VRML files which, in turn, can be embedded into the pdf files (3d pdf). 3d pdf files can be read and visualized by the (freeware) Adobe Reader. Some publishers accept 3d pdf submissions. You can have a look at the sample 3d pdf files at the Jamberoo web pages.

Regards,
Vlad --Boundary_(ID_+Izqm9tuI7kjujE94lnnCg)-- From owner-chemistry@ccl.net Fri Jun 25 09:24:00 2010 From: "Valia Dimitrova ohtvd:+:chem.uni-sofia.bg" To: CCL Subject: CCL:G: problem with imaginery frequency and keyword modredundant in G03 Message-Id: <-42189-100623105229-3808-Aw0BmKX4DQecFfjav4bQsA() server.ccl.net> X-Original-From: "Valia Dimitrova" Content-Type: multipart/alternative; boundary="0623_1445_49_PART-BREAK" Date: Wed, 23 Jun 2010 17:45:49 +0300 MIME-Version: 1.0 Sent to CCL by: "Valia Dimitrova" [ohtvd_-_chem.uni-sofia.bg] --0623_1445_49_PART-BREAK Content-Type: text/plain; charset="us-ascii" Hi Ol Ga, thank you very much for you answer. I have to use modredundant option, because I have to get definite geometry, if I don't use modredundant one of molecules is rotate in a way which is not my aim. Therefore I freeze two dihedral angles, and I done optimization , and at the end of out file I have 1 imaginery frequency, I have to calculate hydrogen bond energy so I have to find way to remove this frequency. I wonder if there is any way in which I can remove this frequency. best regards V. Nikolova -----Original Message----- > From: "Ol Ga eurisco1|a|pochta.ru" To: "Nikolova, Valia Kirilova " Date: Tue, 22 Jun 2010 14:15:58 -0400 Subject: CCL:G: problem with imaginery frequency and keyword modredundant in G03 Sent to CCL by: "Ol Ga" [eurisco1||pochta.ru] Dear Valya Nikolova, If the structure is not FULLY optimized, you can observe imaginary frequency or frequencies as well as it is possible that non-optimized structure has not any imaginary frequency. To remove imaginary frequency you should perform geometry opt without constraints. It is better to think why do you need modredundant option. Possible you can just ignore imag freq. It depends strongly on your aim or subject of your research etc. Sincerely, Ol Ga > From: "Valya Nikolova ohtvd..chem.uni-sofia.bg" > Sent: Tuesday, June 22, 2010 6:36 PM > To: "Ga, Ol " > Subject: CCL: problem with imaginery frequency and keyword modredundant in G03 > > Sent to CCL by: "Valya Nikolova" [ohtvd:chem.uni-sofia.bg] > hello, > I will be very appreciate, if someone can help me. I done hydrogen bonded complexes with option modredundant, and I have 1 imaginery frequency in the out file. How can I remove it, and is it exists every time when you work with modredundant. > thanck you in advancehttp://www.ccl.net/cgi-bin/ccl/send_ccl_message [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/chemistry/sub_unsub.shtml][http://www.ccl.net/][http://www.ccl.net/jobs][http://server.ccl.net/chemistry/announcements/conferences/][http://www.ccl.net/chemistry/searchccl/index.shtml]http://www.ccl.net/spammers.txt [http://www.ccl.net/spammers.txt][http://www.ccl.net/chemistry/aboutccl/instructions/] --0623_1445_49_PART-BREAK Content-Type: text/html; charset="us-ascii"
Hi Ol Ga,
thank you very much for you answer. I have to use modredundant option, because I have to get definite geometry, if I don't use modredundant one of molecules is rotate in a way which is not my aim. Therefore I freeze two  dihedral angle s, and I done optimization , and at the end of out file I have 1 imaginery frequency, I have to calculate hydrogen bond energy so I have to find way to remove this frequency. I wonder if there is any way in which I can remove this frequency.
best regards V. Nikolova
-----Original Message-----
> From: "Ol Ga eurisco1|a|pochta.ru" <owner-chemistry_._ccl.net>
To: "Nikolova, Valia Kirilova " <ohtvd_._chem.uni-sofia.bg>
Date: Tue, 22 Jun 2010 14:15:58 -0400
Subject: CCL:G: problem with imaginery frequency and keyword modredundant in G03


Sent to CCL by: "Ol  Ga" [eurisco1||pochta.ru]
Dear Valya  Nikolova,

If the structure is not FULLY optimized, you can observe imaginary frequency or frequencies as well as it is possible that non-optimized structure has not any imaginary frequency.
To remove imaginary frequency you should perform geometry opt without constraints.
It is better to think why do you need  modredundant  option. Possible you can just ignore imag freq. It depends strongly on your aim or subject of your research etc.

Sincerely,
Ol Ga

> From: "Valya Nikolova ohtvd..chem.uni-sofia.bg" <owner-chemistry++ccl.net>
> Sent: Tuesday, June 22, 2010 6:36 PM
> To: "Ga, Ol " <eurisco1++pochta.ru>
> Subject: CCL: problem with imaginery frequency and keyword modredundant in G03
>
> Sent to CCL by: "Valya  Nikolova" [ohtvd:chem.uni-sofia.bg]
> hello,
> I will be very appreciate, if someone can help me. I done hydrogen bonded complexes with option modredundant, and I have 1 imaginery frequency in the out file. How can I remove it, and is it exists every time when you work with modredundant.
> thanck you in advance




     

     

     

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--0623_1445_49_PART-BREAK-- From owner-chemistry@ccl.net Fri Jun 25 09:59:00 2010 From: "Tamas Gunda tgunda1%x%puma.unideb.hu" To: CCL Subject: CCL: AW: Creating publishable 2D drawings from 3D Z-matrix based input files Message-Id: <-42190-100625040242-10490-1UidyRA/sBPQoQmJHSzGeA(!)server.ccl.net> X-Original-From: "Tamas Gunda" Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Fri, 25 Jun 2010 10:02:35 +0200 MIME-Version: 1.0 Sent to CCL by: "Tamas Gunda" [tgunda1%%puma.unideb.hu] Right, Mol2mol simply squeezes or fully flattens the molecule, good for later experimentation with general 3D modelling programs to create special effects. In my experiences Chem3D makes a good job in creating a 2D drawing: input the molecule, open the ChemDraw pane, and while rotating the molecule file in the 3D pane, it is on-the-fly being converted to a 2D drawing. Tamas E. Gunda University of Debrecen Department of Pharmaceutical Chemistry Debrecen, Hungary ----- Original Message ----- > From: "Wolf-D. Ihlenfeldt wdi^_^xemistry.com" To: "Gunda, Tamas E " Sent: Thursday, June 24, 2010 19:11 PM Subject: CCL: AW: Creating publishable 2D drawings from 3D Z-matrix based input files Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi-x-xemistry.com] I do not think mol2mol does 2D layout, which is, if I understood the original posting correctly, the core of the problem... if you just want to render 3D structures, there are lots of other possibilities, besides mol2mol... > -----Ursprüngliche Nachricht----- > Von: owner-chemistry+wdi==xemistry.com]-[ccl.net [mailto:owner- > chemistry+wdi==xemistry.com]-[ccl.net] Im Auftrag von Jim Kress > ccl_nospam]|[kressworks.com > Gesendet: Donnerstag, 24. Juni 2010 17:22 > An: Ihlenfeldt, Wolf D > Betreff: CCL: Creating publishable 2D drawings from 3D Z-matrix based > input files > > > Sent to CCL by: "Jim Kress" [ccl_nospam%a%kressworks.com] > mol2mol? > > http://www.gunda.hu/mol2mol/index.html > > > Jim > > -----Original Message----- > > From: owner-chemistry+ccl_nospam==kressworks.com : ccl.net > [mailto:owner-chemistry+ccl_nospam==kressworks.com : ccl.net] On Behalf > Of > John McKelvey jmmckel!^!gmail.com > Sent: Thursday, June 24, 2010 8:17 AM > To: Kress, Jim > Subject: CCL: Creating publishable 2D drawings from 3D Z-matrix based > input > files > > > Sent to CCL by: John McKelvey [jmmckel,gmail.com] > Hello, > > I have about 50 MOPAC input structures I need to get into 2D drawings > for publication, obviously multiple drawings on a page. Any > suggestions how to do this? > > Thanks! > > Johnhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Jun 25 10:34:01 2010 From: "Syed Tarique Moin tarisyed() yahoo.com" To: CCL Subject: CCL: coulombic and lennard-jones potential Message-Id: <-42191-100625084413-22884-Z5C0ryyueHrFojM1tx8Jrg/./server.ccl.net> X-Original-From: "Syed Tarique Moin" Date: Fri, 25 Jun 2010 08:44:12 -0400 Sent to CCL by: "Syed Tarique Moin" [tarisyed[*]yahoo.com] Hi CCL users, I am trying to construct the non-bonded parameters e.g coulombic potential and lennard jones potential for a transition metal complex containing a transition metal surrounded by 6 coordinating atom. I want suggestion that how can i get these parameters. Should i scan each bond distance between metal and coordinating and take average. Or can anybody guide me or has some clues about some kind of tutorials. Thanks in advance From owner-chemistry@ccl.net Fri Jun 25 11:31:00 2010 From: "Wolf Ihlenfeldt wdi:+:xemistry.com" To: CCL Subject: CCL: Creating publishable 2D drawings from 3D Z-matrix based input files Message-Id: <-42192-100625095516-20449-VJMCIiEIIQNGJ9jWhkCi4g=server.ccl.net> X-Original-From: Wolf Ihlenfeldt Content-Type: multipart/alternative; boundary=0016367fb73f33bc980489db1e87 Date: Fri, 25 Jun 2010 14:55:04 +0100 MIME-Version: 1.0 Sent to CCL by: Wolf Ihlenfeldt [wdi__xemistry.com] --0016367fb73f33bc980489db1e87 Content-Type: text/plain; charset=UTF-8 Once again: The problem is not rendering a 3D model to an image (there are lots of applications for that), but performing a 2D structure layout from data files which only have 3D atomic coordinates (and no bonding information, to make this even more interesting). Tools which can do that are scarce. So far, only the proposed Cactvs and ChemAxon routes appear to be viable. > From what I see on the website cited below, JMolEditor is no help with this problem, either. On Fri, Jun 25, 2010 at 10:17 AM, Vladislav Vassiliev vladislav.vassiliev** anu.edu.au wrote: > Hi John, > > Jamberoo, http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html, > can read in several formats as Z-matrix. It can also produce 2D pictures as > well as VRML files which, in turn, can be embedded into the pdf files (3d > pdf). 3d pdf files can be read and visualized by the (freeware) Adobe > Reader. Some publishers accept 3d pdf submissions. You can have a look at > the sample 3d pdf files at the Jamberoo web pages. > > Regards, > Vlad --0016367fb73f33bc980489db1e87 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Once again: The problem is not rendering a 3D model to an image (there = are lots of applications for that), but performing a 2D structure layout fr= om data files which only have 3D atomic coordinates (and no bonding informa= tion, to make this even more interesting). Tools which can do that are scar= ce. So far, only the proposed Cactvs and ChemAxon routes appear to be viabl= e.

From what I see on the website cited below, JMolEditor is no help with = this problem, either.

On Fri, Jun 25, 201= 0 at 10:17 AM, Vladislav Vassiliev vladislav.vassiliev**anu.edu.au <owner-chemistry##ccl.net> wrote:
Hi John,

J= amberoo, http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/= index.html, can read in several formats as Z-matrix. It can also produc= e 2D pictures as well as VRML files which, in turn, can be embedded into th= e pdf files (3d pdf). 3d pdf files can be read and visualized by the (freew= are) Adobe Reader. Some publishers accept 3d pdf submissions. You can have = a look at the sample 3d pdf files at the Jamberoo web pages.

Regards,
Vlad

--0016367fb73f33bc980489db1e87-- From owner-chemistry@ccl.net Fri Jun 25 12:07:01 2010 From: "Jamel MESLAMANI meslamani*ulp.u-strasbg.fr" To: CCL Subject: CCL: are there any good free 3D conformations generators? Message-Id: <-42193-100625081542-1534-WCu6x8M5IuXGs45+uZ/D9A]![server.ccl.net> X-Original-From: Jamel MESLAMANI Content-Type: multipart/alternative; boundary="------------070406010302030305010501" Date: Fri, 25 Jun 2010 14:16:36 +0200 MIME-Version: 1.0 Sent to CCL by: Jamel MESLAMANI [meslamani/a\ulp.u-strasbg.fr] This is a multi-part message in MIME format. --------------070406010302030305010501 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi andrew, You can try Frog2 : http://bioserv.rpbs.jussieu.fr/cgi-bin/Frog2 Frog: a FRee Online druG 3D conformation generator. Leite et al. Nucleic Acid Res., 2007 Jul;35(Web Server issue):W568-72. Epub 2007 May 7. doi:10.1093/nar/gkm289 Andrew Voronkov drugdesign-x-yandex.ru wrote: > Sent to CCL by: Andrew Voronkov [drugdesign[*]yandex.ru] > Dear CCL users, can you please recommend the adequate free 3D generators > like open source or generators which are free for all types of > organizations? > I have tried this software: > http://users.abo.fi/mivainio/balloon/ > but to say the truth quality is not very good (like corrupted aromaticity). > > Sincerely yours, > Andrew> > > --------------070406010302030305010501 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi andrew,

You can try Frog2 :   http://bioserv.rpbs.jussieu.fr/cgi-bin/Frog2

Frog: a FRee Online druG 3D conformation generator. Leite et al. Nucleic Acid Res., 2007 Jul;35(Web Server issue):W568-72. Epub 2007 May 7.
doi:10.1093/nar/gkm289


Andrew Voronkov drugdesign-x-yandex.ru wrote: 
Sent to CCL by: Andrew Voronkov [drugdesign[*]yandex.ru]
Dear CCL users, can you please recommend the adequate free 3D generators
like open source or generators which are free for all types of
organizations?
I have tried this software:
http://users.abo.fi/mivainio/balloon/
but to say the truth quality is not very good (like corrupted aromaticity).

Sincerely yours,
AndrewE-mail to subscribers: CHEMISTRY() ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

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--------------070406010302030305010501-- From owner-chemistry@ccl.net Fri Jun 25 12:41:00 2010 From: "Ibrahim Moustafa I.moustafa^^psu.edu" To: CCL Subject: CCL: AutoDock - Kollman charge for protein Message-Id: <-42194-100625114801-10226-Z9vtNUPuEsbdMkVlln6txg*server.ccl.net> X-Original-From: Ibrahim Moustafa Content-type: multipart/alternative; boundary="B_3360311278_20913327" Date: Fri, 25 Jun 2010 11:47:37 -0400 Mime-version: 1.0 Sent to CCL by: Ibrahim Moustafa [I.moustafa,,psu.edu] > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3360311278_20913327 Content-type: text/plain; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable Dear CCL users, I=B9m trying to do some docking using AutoDock 4.2. I need to prepare the protein for the docking and add Kollman charge. I wonder if there is a free software or web server that can reliably do this. I tried to use AutoDockTools but it does not recognize the correct total charge on the protein. For the total charge (-5) on the protein, ADT calculates the total charge (-4). Moreover, checking the charges in the output pdbq file gave a sum of (-3.47 rather than =AD4.0 as reported by ADT). I=B9m not sure what could be the problem; that is why I=B9m looking for an alternative way to prepare the protein for the docking run. Thanks for help, Ibrahim --B_3360311278_20913327 Content-type: text/html; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable AutoDock - Kollman charge for protein Dear CCL users,

I’m trying to do some docking using AutoDock 4.2. I need to prepare t= he protein for the docking and add Kollman charge.
I wonder if there is a free software or web server that can reliably do thi= s.
 I tried to use AutoDockTools but it does not recognize the correct to= tal charge on the protein.
For the total charge (-5) on the protein, ADT calculates the total charge (= -4). Moreover, checking the charges in the output pdbq file gave a sum of (-= 3.47 rather than –4.0 as reported by ADT). I’m not sure what cou= ld be the problem; that is why I’m looking for an alternative way to p= repare the protein for the docking run.


 Thanks for help,
 Ibrahim
  --B_3360311278_20913327-- From owner-chemistry@ccl.net Fri Jun 25 15:10:00 2010 From: "Elaine Meng meng=cgl.ucsf.edu" To: CCL Subject: CCL: AutoDock - Kollman charge for protein Message-Id: <-42195-100625142104-32673-4SIkQgTnrMuCjQ9ThXSLHg]|[server.ccl.net> X-Original-From: "Elaine Meng" Date: Fri, 25 Jun 2010 14:21:03 -0400 Sent to CCL by: "Elaine Meng" [meng~!~cgl.ucsf.edu] Hi Ibrahim, Chimera includes a Dock Prep tool that adds hydrogens and charges, plus can do structure cleanup such as building missing sidechains. The charge set choices include various Amber force field versions. It can write out a Mol2 file, not the AutoDock input format. However, it may still be useful if you can convert the format with some other program. Of course, Chimera is not a web server... http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html The PDBPQR server is another idea, but I'm guessing that would also require converting the format of the output file. http://pdb2pqr-1.wustl.edu/pdb2pqr/ Best, 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 Fri Jun 25 15:44:00 2010 From: "alfredo tlahuice tlahuicef:+:yahoo.com" To: CCL Subject: CCL: Creating publishable 2D drawings from 3D Z-matrix based input files Message-Id: <-42196-100625121106-4135-Jw17QOU1RiSfNmdS5aG23w#server.ccl.net> X-Original-From: alfredo tlahuice Content-Type: multipart/alternative; boundary="0-444507323-1277482258=:57625" Date: Fri, 25 Jun 2010 09:10:58 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: alfredo tlahuice [tlahuicef[]yahoo.com] --0-444507323-1277482258=:57625 Content-Type: text/plain; charset=us-ascii Hi there. I propose to use the xyz coordinates and by using PovRay to render the 2D pictures. If you can use a script on linux you can render a lot of structures in minutes. I hope this can be useful Alfredo Tlahuice. --- On Fri, 6/25/10, Wolf Ihlenfeldt wdi:+:xemistry.com wrote: > From: Wolf Ihlenfeldt wdi:+:xemistry.com Subject: CCL: Creating publishable 2D drawings from 3D Z-matrix based input files To: "Tlahuice, Alfredo " Date: Friday, June 25, 2010, 2:55 PM Once again: The problem is not rendering a 3D model to an image (there are lots of applications for that), but performing a 2D structure layout from data files which only have 3D atomic coordinates (and no bonding information, to make this even more interesting). Tools which can do that are scarce. So far, only the proposed Cactvs and ChemAxon routes appear to be viable. > From what I see on the website cited below, JMolEditor is no help with this problem, either. On Fri, Jun 25, 2010 at 10:17 AM, Vladislav Vassiliev vladislav.vassiliev**anu.edu.au wrote: Hi John, Jamberoo, http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html, can read in several formats as Z-matrix. It can also produce 2D pictures as well as VRML files which, in turn, can be embedded into the pdf files (3d pdf). 3d pdf files can be read and visualized by the (freeware) Adobe Reader. Some publishers accept 3d pdf submissions. You can have a look at the sample 3d pdf files at the Jamberoo web pages. Regards, Vlad --0-444507323-1277482258=:57625 Content-Type: text/html; charset=us-ascii
Hi there.
I propose to use the xyz coordinates and by using PovRay to render the 2D pictures. If you can use a script on linux you can render a lot of structures in minutes.
I hope this can be useful
Alfredo Tlahuice.

--- On Fri, 6/25/10, Wolf Ihlenfeldt wdi:+:xemistry.com <owner-chemistry[*]ccl.net> wrote:

From: Wolf Ihlenfeldt wdi:+:xemistry.com <owner-chemistry[*]ccl.net>
Subject: CCL: Creating publishable 2D drawings from 3D Z-matrix based input files
To: "Tlahuice, Alfredo " <tlahuicef[*]yahoo.com>
Date: Friday, June 25, 2010, 2:55 PM


Once again: The problem is not rendering a 3D model to an image (there are lots of applications for that), but performing a 2D structure layout from data files which only have 3D atomic coordinates (and no bonding information, to make this even more interesting). Tools which can do that are scarce. So far, only the proposed Cactvs and ChemAxon routes appear to be viable.

From what I see on the website cited below, JMolEditor is no help with this problem, either.

On Fri, Jun 25, 2010 at 10:17 AM, Vladislav Vassiliev vladislav.vassiliev**anu.edu.au <owner-chemistry__ccl.net> wrote:
Hi John,

Jamberoo, http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html, can read in several formats as Z-matrix. It can also produce 2D pictures as well as VRML files which, in turn, can be embedded into the pdf files (3d pdf). 3d pdf files can be read and visualized by the (freeware) Adobe Reader. Some publishers accept 3d pdf submissions. You can have a look at the sample 3d pdf files at the Jamberoo web pages.

Regards,
Vlad


--0-444507323-1277482258=:57625-- From owner-chemistry@ccl.net Fri Jun 25 16:19:01 2010 From: "Ol Ga eurisco1^pochta.ru" To: CCL Subject: CCL:G: problem with imaginery frequency and keyword modredundant i Message-Id: <-42197-100625145620-8264-XOLLN/gG9BpZo48+6BN/FQ^-^server.ccl.net> X-Original-From: "Ol Ga" Date: Fri, 25 Jun 2010 14:56:19 -0400 Sent to CCL by: "Ol Ga" [eurisco1 _ pochta.ru] Dear Valya Nikolova, According your explanation you try to calculate hydrogen bond energy methodologically incorrect. Your problem is optimization of structure near shallow potential minima, i.e. something rotate etc., if you are sure that fully optimized structure is not your "definite geometry". Anyway you already have energy (of structure with constrained geometrical parameters). You can already compare it. Sincerely, Ol Ga > From: Valia Dimitrova ohtvd:+:chem.uni-sofia.bg Sent: Wednesday, June 23, 2010 6:45 PM To: Ga, Ol Subject: CCL:G: problem with imaginery frequency and keyword modredundant in G03 Hi Ol Ga, thank you very much for you answer. I have to use modredundant option, because I have to get definite geometry, if I don't use modredundant one of molecules is rotate in a way which is not my aim. Therefore I freeze two dihedral angle s, and I done optimization , and at the end of out file I have 1 imaginery frequency, I have to calculate hydrogen bond energy so I have to find way to remove this frequency. I wonder if there is any way in which I can remove this frequency. best regards V. Nikolova -----Original Message----- > From: "Ol Ga eurisco1|a|pochta.ru" To: "Nikolova, Valia Kirilova " Date: Tue, 22 Jun 2010 14:15:58 -0400 Subject: CCL:G: problem with imaginery frequency and keyword modredundant in G03 Sent to CCL by: "Ol Ga" [eurisco1||pochta.ru] Dear Valya Nikolova, If the structure is not FULLY optimized, you can observe imaginary frequency or frequencies as well as it is possible that non-optimized structure has not any imaginary frequency. To remove imaginary frequency you should perform geometry opt without constraints. It is better to think why do you need modredundant option. Possible you can just ignore imag freq. It depends strongly on your aim or subject of your research etc. Sincerely, Ol Ga > From: "Valya Nikolova ohtvd..chem.uni-sofia.bg" > Sent: Tuesday, June 22, 2010 6:36 PM > To: "Ga, Ol " > Subject: CCL: problem with imaginery frequency and keyword modredundant in G03 > > Sent to CCL by: "Valya Nikolova" [ohtvd:chem.uni-sofia.bg] > hello, > I will be very appreciate, if someone can help me. I done hydrogen bonded complexes with option modredundant, and I have 1 imaginery frequency in the out file. How can I remove it, and is it exists every time when you work with modredundant. > thanck you in advance From owner-chemistry@ccl.net Fri Jun 25 18:47:00 2010 From: "Mark Ellison mellison. . .ursinus.edu" To: CCL Subject: CCL:G: Help with ONIOM calculation Message-Id: <-42198-100625161636-27415-ot6J4rFeXFC3oqHCHwQR0A . server.ccl.net> X-Original-From: "Mark Ellison" Date: Fri, 25 Jun 2010 16:16:34 -0400 Sent to CCL by: "Mark Ellison" [mellison..ursinus.edu] I was wondering if anyone could give me some suggestions for a troublesome two-level ONIOM calculation in Gaussian 03. I am trying to model the hydroboration of a single-walled carbon nanotube. The nanotube consists of about 100 C atoms, linked in aromatic 6-member rings and is the low-level part of the system, treated at the HF/3-21G level. The high-level part of the system is two adjacent 6-member carbon rings, and, where the rings share an edge, one carbon is bonded to an H atom, and the other carbon atom is bonded to a -BH2 group. The high-level part is treated at the B3LYP/6-31+G(d) level. When I run a geometry optimization, the -BH2 and -H (bonded to adjacent carbon atoms) "lean" over toward each other, almost as if the H atom is bridging between the B and the C (a la the bridging H atoms in diborane). The strange thing is that I ran a geometry optimization with the entire system at the B3LYP/6-31+G(d) level, and the -BH2 and -H don't "lean" toward each other--they point slightly away from each other, as you would expect if the C atoms to which they were bound are sp3 hybridized. I have tried a couple of things: --using the geometry result when the entire system was treated at B3LYP/6-31+G(d) as the starting point for the ONIOM calculation --performing an ONIOM calculation with the lower level the same but the higher level at B3LYP/6-31G(d) Both of these gave the same result: H and BH2 "lean" toward each other. When I tried the calculation with B3LYP/6-31+G(d) for the high level and molecular mechanics UFF for the low level, the H and BH2 don't "lean" toward each other. If anyone has any suggestions that they can email to me, that would be most appreciated. Thank you.