From owner-chemistry@ccl.net Fri Sep 14 07:28:00 2007 From: "Ol Ga eurisco1__pochta.ru" To: CCL Subject: CCL: Re : all-electron basis for gd Message-Id: <-35151-070914064128-13383-Z8JgaTTjLqEwfqz3tPA8Mw++server.ccl.net> X-Original-From: "Ol Ga" Date: Fri, 14 Sep 2007 06:41:24 -0400 Sent to CCL by: "Ol Ga" [eurisco1|-|pochta.ru] For Gd in G94 all-electronic basis set is WTBS see it on http://gnode2.pnl.gov/bse/portal From owner-chemistry@ccl.net Fri Sep 14 10:36:00 2007 From: "Nahren Mascarenhas meetnahren,yahoo.com" To: CCL Subject: CCL: simulation Message-Id: <-35152-070914080125-14113-zLrP9BhtLs7d5nt59tzycA(_)server.ccl.net> X-Original-From: "Nahren Mascarenhas" Date: Fri, 14 Sep 2007 08:01:21 -0400 Sent to CCL by: "Nahren Mascarenhas" [meetnahren-#-yahoo.com] Dear CCL Members, I have just started to work on simulation studies. I want to know the exact procedure for performing the same. I have used the following: 1000 steps of Steepest Descent Minimization 1000 steps equiliberation at 300 K followed by 150 ps simulation your advise and suggestions will help me a lot nahren From owner-chemistry@ccl.net Fri Sep 14 11:13:00 2007 From: "fabrice fabrun fgardebien(-)hotmail.com" To: CCL Subject: CCL: Visualization program for Mopac Message-Id: <-35153-070914064700-14090-+rc/yWU3uw3hOZ/q5Aqd9Q a server.ccl.net> X-Original-From: "fabrice fabrun" Date: Fri, 14 Sep 2007 06:46:56 -0400 Sent to CCL by: "fabrice fabrun" [fgardebien,+,hotmail.com] Hello, I am trying to find a visualization program for the molecular orbitals generated using MOPAC (gpt file or wmp/wob files), preferentially running under Linux. Does anyone have some suggestions. Thanks. Fabrice. From owner-chemistry@ccl.net Fri Sep 14 12:46:01 2007 From: "Rick Venable venabler-$-nhlbi.nih.gov" To: CCL Subject: CCL: simulation Message-Id: <-35154-070914124429-17189-9Tyl6CneRRwjmCU0Pp8z3w.:.server.ccl.net> X-Original-From: Rick Venable Content-transfer-encoding: 7bit Content-type: text/plain; charset="US-ASCII" Date: Fri, 14 Sep 2007 12:11:07 -0400 Mime-version: 1.0 Sent to CCL by: Rick Venable [venabler]*[nhlbi.nih.gov] Procedural details tend to be somewhat specific to the program being being used. Major academic simulations packages such as AMBER, CHARMM, GROMOS or GROMACS, and NAMD each have their own respective web sites and/or mailing lists for questions of this nature. AMBER amber.scripps.edu CHARMM www.charmm.org GROMOS www.igc.ethz.ch/gromos/ GROMACS www.gromacs.org NAMD www.ks.uiuc.edu/Research/namd/ -- Rick Venable 5635 FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov On 9/14/07 8:01 AM, "Nahren Mascarenhas meetnahren,yahoo.com" wrote: > > Sent to CCL by: "Nahren Mascarenhas" [meetnahren-#-yahoo.com] > Dear CCL Members, > > I have just started to work on simulation studies. > I want to know the exact procedure for performing the same. > I have used the following: > 1000 steps of Steepest Descent Minimization > 1000 steps equiliberation at 300 K > followed by 150 ps simulation > > > your advise and suggestions will help me a lot > > nahren> From owner-chemistry@ccl.net Fri Sep 14 13:41:00 2007 From: "Rajarshi Guha rguha(-)indiana.edu" To: CCL Subject: CCL: smi23d and patents Message-Id: <-35155-070914131452-19357-EB+uiOpNuFoxdqAKjHQr8g:server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Fri, 14 Sep 2007 13:14:17 -0400 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Rajarshi Guha [rguha#%#indiana.edu] On Aug 22, 2007, at 12:00 PM, Lothar Terfloth lothar.terfloth|,| chemie.uni-erlangen.de wrote: > > Sent to CCL by: Lothar Terfloth [lothar.terfloth,chemie.uni- > erlangen.de] > > Dear all, > > a) SPE is the central step for the generation of a 'rough' set of > 3D coordinates in smi23d. > Following > > http://www.wipo.int/pctdb/en/wo.jsp? > wo=2004003683&IA=WO2004003683&DISPLAY=STATUS > > or > > http://www.wipo.int/pctdb/en/wo.jsp? > wo=2004003683&IA=WO2004003683&DISPLAY=STATUS > > I would assume that there is a patent on the SPE algorithm and its > application. Does this affect smi23d? We have been in contact with Dimitris Agrafiotis (who is the author of the SPE algorithm as well as named on the patent for SPE - US patent 6,571,227. He has stated that we are free to use the algorithm in smi23d. > e) Is mengine based on Pcmodel version 7? ( http:// > www.serenasoft.com ) Yes, the code for mengine is based on PCModel. However there are no issues with respect to patent/copyright for mengine - the source code is freely available under the Apache license ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- A mathematician is a device for turning coffee into theorems. -- P. Erdos From owner-chemistry@ccl.net Fri Sep 14 14:15:00 2007 From: "Rajarshi Guha rguha^-^indiana.edu" To: CCL Subject: CCL: smi23d - web form and web services Message-Id: <-35156-070914131436-19168-NeAHw2AaE3fTxpXeZ5x7Kg---server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Fri, 14 Sep 2007 12:13:04 -0400 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Rajarshi Guha [rguha~!~indiana.edu] We recently announced the availability of smi23d, a 3D coordinate generation tool. It is provided as C source code which needs to be compiled. We have also provided a web form, which allows you to paste SMILES strings or link to a URL representing a SMILES file and get back the 3D coordinates as an SD file. There is a limit of 200 compounds. The web form is available at http://www.chembiogrid.org/cheminfo/ threed/d3 It is based on an underlying web service. The WSDL for the web service is http://rguha.ath.cx:8080/threed/services/Coord3D?wsdl and the Javadocs are at http://cheminfo.informatics.indiana.edu/~rguha/ws/ threed/api/ Example code to access the web service using Python and SOAPpy is import SOAPpy if __name__ == '__main__': s = SOAPpy.WSDL.Proxy('http://rguha.ath.cx:8080/threed/services/ Coord3D?wsdl') smiles = 'CCC' print s.get3DStructure(smiles,1) ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Entropy requires no maintenance. -- Markoff Chaney From owner-chemistry@ccl.net Fri Sep 14 15:12:00 2007 From: "Richard Leo Wood woodx278]=[umn.edu" To: CCL Subject: CCL: simulation Message-Id: <-35157-070914150921-30301-g5ekSJORNpPB41zw5oZ2EA**server.ccl.net> X-Original-From: "Richard Leo Wood" Date: Fri, 14 Sep 2007 15:09:17 -0400 Sent to CCL by: "Richard Leo Wood" [woodx278[A]umn.edu] Hi all, I just want to add that the NAMD list is also available at namd-l|-|ks.uiuc.edu. I also highly recommend the CHARMM forum at www.charmm.org, where one can post questions. Best, Richard Sent to CCL by: Rick Venable [venabler]*[nhlbi.nih.gov] Procedural details tend to be somewhat specific to the program being being used. Major academic simulations packages such as AMBER, CHARMM, GROMOS or GROMACS, and NAMD each have their own respective web sites and/or mailing lists for questions of this nature. AMBER amber.scripps.edu CHARMM www.charmm.org GROMOS www.igc.ethz.ch/gromos/ GROMACS www.gromacs.org NAMD www.ks.uiuc.edu/Research/namd/ From owner-chemistry@ccl.net Fri Sep 14 17:00:01 2007 From: "pragya chohan pragyachohan/a\hotmail.com" To: CCL Subject: CCL:G: help:gussian 03:Error termination via Lnk1e in /nepdisk11/g03/l301.exe Message-Id: <-35158-070914153643-12141-jez0rMeBnwyGQYpA8sfQhA{=}server.ccl.net> X-Original-From: "pragya chohan" Date: Fri, 14 Sep 2007 15:36:39 -0400 Sent to CCL by: "pragya chohan" [pragyachohan---hotmail.com] hi i m new to computational biology.i m doing a simulation in gaussian 03 of popc. i m getting this error: Standard basis: 6-31G(d) (6D, 7F) The combination of multiplicity 1 and 419 electrons is impossible. Error termination via Lnk1e in /nepdisk11/g03/l301.exe pls help asap. my .com file is: %chk=Gaussian B3LYP/6-31G* fopt POPC 1 1 C -0.2510 3.2520 3.3350 O 0.3620 3.9930 2.5940 C -0.1840 1.7630 3.2650 C 1.2750 1.3160 3.6060 C 1.4260 -0.2330 3.8530 C 1.1380 -1.0510 2.6150 C 1.4880 -2.5000 2.8060 C 0.8760 -3.4140 1.7060 C 0.8990 -4.8580 2.0770 C 0.1320 -5.6290 0.9810 C -0.1290 -7.1000 1.5280 C 1.1270 -7.8660 1.9340 C 0.7830 -9.3600 2.1530 : H -5.2550 -14.8970 5.3250 <2 lines blank> From owner-chemistry@ccl.net Fri Sep 14 21:51:00 2007 From: "ramchemi ramchemi]^[intnet.mu" To: CCL Subject: CCL:G: help:gussian 03:Error termination via Lnk1e in /nepdisk11/g03/l301.exe Message-Id: <-35159-070914214525-24703-h/982r25HND5dlc134li0w:server.ccl.net> X-Original-From: "ramchemi" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 1 Jan 1999 00:06:01 -0800 MIME-Version: 1.0 Sent to CCL by: "ramchemi" [ramchemi-.-intnet.mu] there is a problem with the 1 1 as charge and multiplicity you should check ----- Original Message ----- > From: "pragya chohan pragyachohan/ahotmail.com" To: "Ramasami, Ponnadurai " Sent: Friday, September 14, 2007 11:36 AM Subject: CCL:G: help:gussian 03:Error termination via Lnk1e in /nepdisk11/g03/l301.exe > > Sent to CCL by: "pragya chohan" [pragyachohan---hotmail.com] > hi > i m new to computational biology.i m doing a simulation in gaussian 03 of popc. > i m getting this error: > Standard basis: 6-31G(d) (6D, 7F) > The combination of multiplicity 1 and 419 electrons is impossible. > Error termination via Lnk1e in /nepdisk11/g03/l301.exe > pls help asap. > my .com file is: > > %chk=Gaussian > B3LYP/6-31G* fopt > > POPC > > 1 1 > C -0.2510 3.2520 3.3350 > O 0.3620 3.9930 2.5940 > C -0.1840 1.7630 3.2650 > C 1.2750 1.3160 3.6060 > C 1.4260 -0.2330 3.8530 > C 1.1380 -1.0510 2.6150 > C 1.4880 -2.5000 2.8060 > C 0.8760 -3.4140 1.7060 > C 0.8990 -4.8580 2.0770 > C 0.1320 -5.6290 0.9810 > C -0.1290 -7.1000 1.5280 > C 1.1270 -7.8660 1.9340 > C 0.7830 -9.3600 2.1530 > : > H -5.2550 -14.8970 5.3250 > <2 lines blank> >