From owner-chemistry@ccl.net Mon Jul 26 02:39:00 2010 From: "Carlos F. Lagos carlos- -cbuc.cl" To: CCL Subject: CCL: autodock parameters Message-Id: <-42350-100726023823-11537-eDuMNNuoiR/2DOqXv2k/6Q.@.server.ccl.net> X-Original-From: "Carlos F. Lagos" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 26 Jul 2010 02:38:02 -0400 MIME-Version: 1.0 Sent to CCL by: "Carlos F. Lagos" [carlos]|[cbuc.cl] Hello Matt: Here are some examples 1) Zhang et al, DOVIS implementation (BMC Bioinformatics 2008, 9:126) used this config ga_pop_size 200 ga_num_evals 250000 ga_run 10 2) Prakhov et al, VSDocker (Bioinformatics 2010 26(10):1374-1375) used this one ga_pop_size 150 ga_num_evals 270000 ga_run 10 You can also consider receptor flexibility (AD4 allowed) QF Carlos F. Lagos Centre for Bioinformatics CBUC, Faculty of Biological Sciences P. Universidad Catolica de Chile Portugal 49 Zocalo I 8330025 Santiago-Chile Phone:+56 2 3541911 -----Mensaje original----- De: owner-chemistry+carlos==cbuc.cl ~~ ccl.net [mailto:owner-chemistry+carlos==cbuc.cl ~~ ccl.net] En nombre de Matthew Clark mclark**pharmatrope.com Enviado el: Domingo, 25 de Julio de 2010 16:33 Para: Lagos, Carlos F Asunto: CCL: autodock parameters All, Is there an accepted set of settings for screening large databases of compounds for autodock? e.g. ga_run, ga_num_evals, ga_pop_size? I'm looking to screen about 1M compounds, and need a recommendation for settings that are fast, yet considered 'adequate'. I do have access to about 100 cpu's for this project, just to let you know of the computing capacity to go with the setting recommendations. Matt ________________________________ Matthew Clark, Ph. D. CIO Pharmatrope Ltd 610 772 4652 mclark]^[pharmatrope.com __________ Informacin de ESET NOD32 Antivirus, versin de la base de firmas de virus 5311 (20100725) __________ ESET NOD32 Antivirus ha comprobado este mensaje. http://www.eset.com __________ Informacion de ESET NOD32 Antivirus, version de la base de firmas de virus 5311 (20100725) __________ ESET NOD32 Antivirus ha comprobado este mensaje. http://www.eset.com From owner-chemistry@ccl.net Mon Jul 26 05:44:01 2010 From: "Anton Nizovtsev nanto=mail.ru" To: CCL Subject: CCL: O2 (1sigma+g) Message-Id: <-42351-100726053218-485-yC5aiGwXsv5aHEvyCxykkQ|server.ccl.net> X-Original-From: "Anton Nizovtsev" Date: Mon, 26 Jul 2010 05:32:17 -0400 Sent to CCL by: "Anton Nizovtsev" [nanto::mail.ru] Dear All, Is it correct to say that the 1sigma+g state of molecular oxygen is considered if the restricted single-reference methods (RDFT, RMPn, RCCSD etc) are used? Which methods (if it possible) can be used for this task besides multireference ones? Thanks in advance, Anton From owner-chemistry@ccl.net Mon Jul 26 06:18:00 2010 From: "Mark Onyango mark.onyango]|[tg.fh-giessen.de" To: CCL Subject: CCL:G: "Guess=Alter" not executed Message-Id: <-42352-100726061349-27068-GHRDN5EK5qrRKAanIBUWng- -server.ccl.net> X-Original-From: "Mark Onyango" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 26 Jul 2010 12:13:38 +0200 MIME-Version: 1.0 Sent to CCL by: "Mark Onyango" [mark.onyango---tg.fh-giessen.de] Hi Jane, could you please give us some information on your input deck? What kind of job do you want to run? If I want to alter the guess i first run a guess=(only,save) job to analyze which orbitals to switch. Afterwards I run a guess=(read,alter) job to switch the orbitals. This worked for me so far. You could also try to use the nosymm keyword (http://www.ch.ic.ac.uk/robb/casscf_benzene_handout.php). Best, Mark > Hi All, > > I have a confusion about the "*Guess=Alter*" command in Gaussian03. I used > this command to promote one unpaired electron from sigma orbital to pi > orbital, in order to change the molecule form sigma radical to pi radical. > However, the energy, charge and spin density are totally the same as > before. > Seems like it is not executed at all. > > I am pretty sure that I switched the correct orbitals and I kept the > molecule under Cs symmetry all the time. Does anyone know what caused this > failure? > > Thank you very much! > > Jane > From owner-chemistry@ccl.net Mon Jul 26 08:35:01 2010 From: "Daniel Jana dfjana|*|gmail.com" To: CCL Subject: CCL:G: Gaussian 09 compatibility Message-Id: <-42353-100726083328-23183-pU1W81ccLlMQcAjzV1T3fA ~ server.ccl.net> X-Original-From: Daniel Jana Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 26 Jul 2010 14:33:16 +0200 MIME-Version: 1.0 Sent to CCL by: Daniel Jana [dfjana]^[gmail.com] Hello, Change to a newer version of Molden. Somewhere in version 4.7, if I'm not mistaken, there was an update to fix that. Molden doesn't number version below the minor, so there are 4.7 versions that still do not work properly. Current version (4.9) works fine. Cheers, Daniel On 23 July 2010 19:16, Randy P Sabatini rsabatin%mail.rochester.edu wrote: > > Sent to CCL by: "Randy P Sabatini" [rsabatin|*|mail.rochester.edu] > Does the graphical program Molden work with Gaussian 09? Ever since I made the switch from 03 to 09, I haven't been able to view frequencies or orbital populations with Molden. All I get when I open the file are a bunch of plus signs where the atoms should be. Thanks.>      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> > > From owner-chemistry@ccl.net Mon Jul 26 12:23:00 2010 From: "Jamin Krinsky jamink**berkeley.edu" To: CCL Subject: CCL:G: "Guess=Alter" not executed Message-Id: <-42354-100726122212-31782-mS9ApYfjGbfLXSKjJNKWxA|-|server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: multipart/alternative; boundary=00c09f9b07829c8c50048c4cc847 Date: Mon, 26 Jul 2010 09:21:57 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink,berkeley.edu] --00c09f9b07829c8c50048c4cc847 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Jane, If the orbitals you are switching are in the same irreducible representatio= n in the point group of your molecule (or if you do not have symmetry), altering the orbital ordering will not change the SCF result, because the algorithm is trying to give you the ground state. Someone suggested using "guess=3Donly" and looking at the result. This is a good idea because you c= an verify that the "guess=3Dalter" keyword worked, but when you converge that wavefunction it will collapse to your previous result, assuming your previous result was not a spurious local minimum (in orbital space). Assuming you are using DFT here, note that the theory is only defined at th= e ground state for each irreducible rep. Regards, Jamin 2010/7/25 =E6=AE=B7=E5=81=A5 janeyin600|*|gmail.com > Hi All, > > I have a confusion about the "*Guess=3DAlter*" command in Gaussian03. I u= sed > this command to promote one unpaired electron from sigma orbital to pi > orbital, in order to change the molecule form sigma radical to pi radical= . > However, the energy, charge and spin density are totally the same as befo= re. > Seems like it is not executed at all. > > I am pretty sure that I switched the correct orbitals and I kept the > molecule under Cs symmetry all the time. Does anyone know what caused thi= s > failure? > > Thank you very much! > > Jane > --=20 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 --00c09f9b07829c8c50048c4cc847 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Jane,
If the orbitals you are switching are in the same irreducible r= epresentation in the point group of your molecule (or if you do not have sy= mmetry), altering the orbital ordering will not change the SCF result, beca= use the algorithm is trying to give you the ground state. Someone suggested= using "guess=3Donly" and looking at the result. This is a good i= dea because you can verify that the "guess=3Dalter" keyword worke= d, but when you converge that wavefunction it will collapse to your previou= s result, assuming your previous result was not a spurious local minimum (i= n orbital space). Assuming you are using DFT here, note that the theory is = only defined at the ground state for each irreducible rep.
Regards,
Jamin


2010/7/25 =E6=AE=B7= =E5=81=A5 janeyin600|*|gmail.com <owner-chemistry-.-ccl= .net>
Hi All,
=C2=A0
I have a confusion about the "Guess=3DAlter" command = in Gaussian03. I used this command to promote=C2=A0one unpaired electron fr= om sigma orbital to pi orbital, in order to change the molecule form sigma = radical to pi radical. However, the energy, charge and spin density are tot= ally the same as before. Seems like it is not executed at all.
=C2=A0
I am pretty sure that I switched the correct orbitals and I kept the m= olecule under Cs=C2=A0symmetry all the time. Does anyone know=C2=A0what cau= sed this failure?=C2=A0
=C2=A0
Thank you very much!
=C2=A0
Jane



--
Jamin L Krinsky, Ph.D.<= br>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

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