From chemistry-request@server.ccl.net Mon Apr 29 05:31:06 2002 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3T9UZA16860 for ; Mon, 29 Apr 2002 05:31:05 -0400 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 1727RG-00075Q-00; Mon, 29 Apr 2002 09:27:18 +0000 Date: Mon, 29 Apr 2002 09:27:18 +0000 (GMT) From: Szilveszter Juhos To: Hunter Hunts cc: ccl Subject: Re: CCL:Running autodock jobs in succesion In-Reply-To: <3CCA2848.3060000@hsc.usf.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sat, 27 Apr 2002, Hunter Hunts wrote: > Can anyone tell me how to set up serveral docking jobs at one time and > then allow the computer to exicute them one after another? You can use condor even on a single CPU machine ( http://www.cs.wisc.edu/condor/ )but it is an overkill in this case. If you do some shell scripting as mentioned do not forget to write "wait" after the jobs. Otherwise all the jobs will be launched at once and likely that is not what you want. Also using "screen" and "tee" can be more convenient than nohup. Launch a screen like: $ screen -S autodock [than launch your jobs here] $ autodockjobs.sh ..... |tee output [press Ctrl-A D to detach screen ] logout than when you are logging in next morning or from a remote machine or from dialup etc $ screen -Ax autodock will give you back the screen as you left it. Hope it helps: Szilva From chemistry-request@server.ccl.net Mon Apr 29 06:02:56 2002 Received: from relay.unizar.es ([155.210.3.21]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3TA2lA17534 for ; Mon, 29 Apr 2002 06:02:48 -0400 Received: from celes.unizar.es (celes.unizar.es [155.210.11.15]) by relay.unizar.es (8.11.1/8.11.1) with ESMTP id g3TA2kW05400; Mon, 29 Apr 2002 12:02:48 +0200 (MET DST) Received: from there (santiago@[155.210.93.83]) by celes.unizar.es (8.11.1/8.11.1) with SMTP id g3TA6Hx23880; Mon, 29 Apr 2002 12:06:18 +0200 (MET DST) Message-Id: <200204291006.g3TA6Hx23880@celes.unizar.es> Content-Type: text/plain; charset="iso-8859-1" From: Santiago Cuesta <405137@docto.unizar.es> Reply-To: 405137@docto.unizar.es Organization: Ciencias To: "J. Zheng" Subject: CCL:ask for workshop of charmm or linux cluster. Date: Mon, 29 Apr 2002 12:02:32 +0200 X-Mailer: KMail [version 1.3.2] Cc: chemistry@ccl.net MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Virus-Scanned: TAMIZ + Sophos en unizar.es Hi !! Maybe this page will help you: http://www.ch.embnet.org/MD_tutorial/ yours sincerely: Santiago Cuesta ----------------------------------- Santiago Cuesta Lopez Predoctoral Student Dep. Fisica de la Materia Condensada. Universidad de Zaragoza (Spain) e-mail: 405137@docto.unizar.es phone: 669191967 From chemistry-request@server.ccl.net Mon Apr 29 14:00:10 2002 Received: from hsc.usf.edu ([131.247.67.157]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g3TI0AA26684 for ; Mon, 29 Apr 2002 14:00:10 -0400 Received: through eSafe SMTP Relay 1019577668; Mon Apr 29 13:57:02 2002 Received: from mindless.com (out.moffitt.usf.edu [131.247.182.200]) by hsc.usf.edu (8.9.3+Sun/8.9.3) with ESMTP id NAA11851 for ; Mon, 29 Apr 2002 13:59:56 -0400 (EDT) Message-ID: <3CCD8A21.C212BE56@mindless.com> Date: Mon, 29 Apr 2002 14:00:01 -0400 From: David Smith X-Mailer: Mozilla 4.78 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: pymol on win95 and color by EP Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear cclr's, I have installed pymol on windows 95 and I get an error "... GLU32.* expects a newer version of windows." Does anyone know a work around for this? Also, I posted a message asking, how to color a surface by electrostatic potential in pymol and havent yet got a reply... so I thought I'd ask again? Thanks guys. Dave From chemistry-request@server.ccl.net Mon Apr 29 17:03:39 2002 Received: from helix.nih.gov ([128.231.2.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3TL3dA29410 for ; Mon, 29 Apr 2002 17:03:39 -0400 Received: (from mn1@localhost) by helix.nih.gov (8.11.6/8.11.6) id g3TL3Xe6979236; Mon, 29 Apr 2002 17:03:33 -0400 (EDT) Date: Mon, 29 Apr 2002 17:03:33 -0400 From: "M. Nicklaus" To: CHEMISTRY@ccl.net cc: "M. Nicklaus" Subject: Announcement: Online SMILES Generator - NEW VERSION Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII A new, expanded version of the Online SMILES Translator service is available on both servers of the Erlangen/Bethesda Data and Online Services. This service is primarily designed to allow Unique SMILES (USMILES) string generation from a variety of input formats and methods: - Direct drawing of a structure in the Java Molecular Editor - Cut-and-past of an existing SMILES string - Submission of single- and multiple-structure files in SDF, PDB, MOL, SMILES (.txt) format (in fact, any input format CACTVS understands). Instead of USMILES, you can also specify SDF, PDB or MOL as the output format for the conversion. Please note that the Unique SMILES definition used in our service is the one published by Daylight in 1989, which is the only one currently publicly available as far as we know. (D. Weininger, A. Weininger, and J.L. Weininger, SMILES. 2. Algorithm for Generation of Unique SMILES Notation, J. Chem. Inf. Comput. Sci. 1989, 29, 97-101.) Dave Weininger promised us to post the current USMILES definition on Daylight's web site. When this happens, we'll have a look at updating our algorithms. The URLs of the German and U.S. servers are, respectively: http://www2.chemie.uni-erlangen.de/services/translate/ http://cactus.nci.nih.gov/services/translate/ Please read the service's Help text for user instructions and some additional information. Thank goes to Frank Oellien of the Computer Chemistry Center, University of Erlangen-Nuremberg, Germany, for implementing this service. For feedback and bug reports, please e-mail to: Frank Oellien and/or Marc Nicklaus . As always, other services that you may find useful are available on our servers at the following URLs: http://www2.chemie.uni-erlangen.de/services/ http://cactus.nci.nih.gov Enjoy! Marc ------------------------------------------------------------------------ Marc C. Nicklaus, Ph.D. NIH/NCI at Frederick E-mail: mn1@helix.nih.gov Bldg 376, Rm 207 Phone: (301) 846-5903 376 Boyles Street Fax: (301) 846-6033 FREDERICK, MD 21702 USA Head, Computer-Aided Drug Design MiniCore Facility Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Mon Apr 29 10:16:36 2002 Received: from so.sd.lionbioscience.com ([209.68.255.43]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3TEGZA22082 for ; Mon, 29 Apr 2002 10:16:35 -0400 Received: from tempest.sd.lionbioscience.com (tempest.sd.lionbioscience.com [10.8.0.8]) by so.sd.lionbioscience.com (8.11.3/8.11.3) with ESMTP id g3TEG2V22612 for ; Mon, 29 Apr 2002 07:16:02 -0700 (PDT) Received: by tempest.sd.lionbioscience.com with Internet Mail Service (5.5.2653.19) id ; Mon, 29 Apr 2002 07:15:43 -0700 Message-ID: From: Stephen Bowlus To: "'chemistry@ccl.net'" Subject: Mopac with Cygwin Date: Mon, 29 Apr 2002 07:15:43 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C1EF88.591DF210" 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. ------_=_NextPart_001_01C1EF88.591DF210 Content-Type: text/plain; charset="iso-8859-1" I am trying to run Mopac 6 on a P3/Win2K machine under Cygwin. Set up for 20 heavy/30 light atoms and without ESP, the program compiles with g77 with only 2 small complaints. Test runs invoked by redirection (mopac < input > output) end with a segmentation fault. The stackdump gives an error about a status access violation. Does anyone have experience with mopac or similar packages and Cygwin or g77? I have no idea what I need to correct to get runnable code. Thanks in advance, Steve *************************************************************** Stephen B. Bowlus, Ph.D. Senior Computational Scientist LION bioscience, Inc. Stephen.Bowlus@lionbioscience.com 9880 Campus Point Dr. Phone: (858) 410-6542 San Diego, CA 92121 Fax: (858) 410-6665 *************************************************************** ------_=_NextPart_001_01C1EF88.591DF210 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Mopac with Cygwin

I am trying to run Mopac 6 on a P3/Win2K machine = under Cygwin.  Set up for 20 heavy/30 light atoms and without ESP, = the program compiles with g77 with only 2 small complaints.  Test = runs invoked by redirection (mopac < input > output) end with a = segmentation fault.  The stackdump gives an error about a status = access violation.

Does anyone have experience with mopac or similar = packages and Cygwin or g77?  I have no idea what I need to correct = to get runnable code.

Thanks in advance,
Steve

***************************************************************=
Stephen B. Bowlus, Ph.D.
Senior Computational Scientist    =

LION bioscience, = Inc.         = Stephen.Bowlus@lionbioscience.com
9880 Campus Point = Dr.           &nb= sp;         Phone: (858) = 410-6542
San Diego, CA = 92121           &= nbsp;           &= nbsp; Fax: (858) 410-6665
***************************************************************=



------_=_NextPart_001_01C1EF88.591DF210-- From chemistry-request@server.ccl.net Mon Apr 29 12:00:52 2002 Received: from lua.ifi.unicamp.br ([143.106.6.13]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3TG0pA23994 for ; Mon, 29 Apr 2002 12:00:51 -0400 Received: by lua.ifi.unicamp.br (Postfix, from userid 106) id 0A7FEA952; Mon, 29 Apr 2002 13:00:40 -0300 (BRT) Received: from posdyn11.ifi.unicamp.br (posdyn11.ifi.unicamp.br [143.106.128.205]) by lua.ifi.unicamp.br (Postfix) with ESMTP id 25B0F5501 for ; Mon, 29 Apr 2002 13:00:39 -0300 (BRT) Message-Id: <5.1.0.14.0.20020429124821.00aa14c8@lua.ifi.unicamp.br> X-Sender: dasf@lua.ifi.unicamp.br X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Mon, 29 Apr 2002 13:02:55 -0300 To: CHEMISTRY@ccl.net From: "Demetrio A. da Silva Filho" Subject: GVB calculation in Gaussian'98 Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_1303687==_.ALT" X-AntiVirus: scanned for viruses by AMaViS 0.2.1 (http://amavis.org/) --=====================_1303687==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCL'ers, I am trying to perform a GVB calculation in Gaussian'98. The basic idea is to create just one GVB pair taking one electron from HOMO-1 one from LUMO. All the orbitals below the pair will be considered as closed shells and will not enter in the calculation. The system will be forced to be singlet. I was able to run that calculation in GAMESS, but the results are not consistent, so I want to do the same calculation in Gaussian'98. But I could not figure out which keywords I must use in order to do the same thing using Gaussian'98. Using Gamess, I just need to run a Hartree-Fock calculation to have a guess for the orbitals and then I use the keywords $SCF NCO=88 NSETO=2 NO(1)=1,1 $END To create the GVB pair and, freezing all orbitals below the HOMO and the keywords: $GUESS GUESS=moread norb=90 NORDER=1 $END $guess iorder(88)=89 iorder(89)=88 $end To change the HOMO-1 orbital (N=88) into HOMO (N=89). Then, at the end, I will have just one GVB pair composed by an electron > from HOMO-1 and one from LUMO. Does anybody knows how can I do the same thing using Gaussian'98? Thanks in advance and have a nice day! Demetrio Filho --=====================_1303687==_.ALT Content-Type: text/html; charset="us-ascii" Dear CCL'ers,

I am trying to perform a GVB calculation in Gaussian'98. The basic idea is to create
just one GVB pair taking one electron from HOMO-1 one from LUMO. All the orbitals below the pair
will be considered as closed shells and will not enter in the calculation. The system will be forced to be singlet.

I was able to run that calculation in GAMESS, but the results are not consistent, so
I want to do the same calculation in Gaussian'98. But I could not figure out which keywords I must use in order
to do  the same thing using Gaussian'98.

Using Gamess, I just need to run a Hartree-Fock calculation to have a guess for the orbitals
and then I use the keywords

$SCF NCO=88 NSETO=2 NO(1)=1,1 $END

To create the GVB pair and, freezing all orbitals below the HOMO and the keywords:

$GUESS  GUESS=moread norb=90 NORDER=1 $END                                    
$guess iorder(88)=89 iorder(89)=88 $end                                       

To change the HOMO-1 orbital (N=88) into HOMO (N=89).

Then, at the end, I will have just one GVB pair composed by an electron
> from HOMO-1 and one from LUMO.

Does anybody knows how can I do the same thing using Gaussian'98?

Thanks in advance and have a nice day!

Demetrio Filho
 --=====================_1303687==_.ALT-- From chemistry-request@server.ccl.net Mon Apr 29 17:08:33 2002 Received: from mailhub1.otago.ac.nz ([139.80.64.218]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3TL8WA29677 for ; Mon, 29 Apr 2002 17:08:32 -0400 Received: (from root@localhost) by mailhub1.otago.ac.nz (8.10.1/8.10.1) id g3TL8Kw24350 for chemistry@ccl.net; Tue, 30 Apr 2002 09:08:20 +1200 Received: from alkali.otago.ac.nz (alkali.otago.ac.nz [139.80.16.4]) by mailhub1.otago.ac.nz (8.10.1/8.10.1) with ESMTP id g3TL8Ja24312 for ; Tue, 30 Apr 2002 09:08:19 +1200 From: timr@alkali.otago.ac.nz Message-Id: <200204292108.g3TL8Ja24312@mailhub1.otago.ac.nz> Received: from ALKALI/SpoolDir by alkali.otago.ac.nz (Mercury 1.40); 30 Apr 102 09:08:18 +1200 Received: from SpoolDir by ALKALI (Mercury 1.41); 30 Apr 102 09:08:12 +1200 Organization: University of Otago To: chemistry@ccl.net Date: Tue, 30 Apr 2002 09:08:09 +1200 MIME-Version: 1.0 X-scanner: scanned by Inflex 1.0.9 - (http://pldaniels.com/inflex/) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: printing of orbital symmetries Priority: normal X-mailer: Pegasus Mail for Win32 (v3.12b) Hi listers, When I run jobs on ferrocene in d5h symmetry, the initial guess orbital symmetries and final orbital symmetries are printed. When I run a calc in d5d symmetry the orbital symmetries are never printed. I need them to be printed so then I can determine excited state symmetries etc. Why are they not printed? I am using exactly the same input for both (including #P and pop=full), bar the atom coordinates of course. By the way, the program correctly determines that it is d5d. Cheers in advance, Tim ------- End of forwarded message ------- ------------------------------- Tim Robinson Vikings Group Department of Chemistry University of Otago tel 64 3 479 7929 fax 64 3 479 7906 timr@alkali.otago.ac.nz