From owner-chemistry@ccl.net Fri Jan 18 03:33:00 2008 From: "Sebastian Rohrer s.rohrer-x-tu-bs.de" To: CCL Subject: CCL: InChI webservices/search Message-Id: <-36066-080118032739-32113-9286R8MfinECTAe7UrbDWQ[a]server.ccl.net> X-Original-From: Sebastian Rohrer Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 18 Jan 2008 09:27:52 +0100 MIME-Version: 1.0 Sent to CCL by: Sebastian Rohrer [s.rohrer/a\tu-bs.de] Hi Hans, the PubChem Poweruser Gateway (PUG) in combination with Entrez e-utils is extremely powerful for the tasks you want to do. See http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html and ftp://ftp.ncbi.nlm.nih.gov/*pubchem*/specifications/*pubchem*_pug.pdf for details. The documentation for PUG is not very extensive so far.Lookily Rich Apodaca wrote some very informative posts on his blog about PUG that I found extremely useful: http://depth-first.com/articles/2007/06/04/hacking-pubchem-power-user-gateway http://depth-first.com/articles/2007/08/14/java-interface-to-pubchems-power-user-gateway Best regards, Sebastian Hans Himmler contact.openchemsoft],[openchemsoft.eu wrote: > Sent to CCL by: "Hans Himmler" [contact.openchemsoft_._openchemsoft.eu] > HI, > > I look for internet URLs that offer InChI code (name/key) related webservices (like e.g. ChemSpider). > I am also interested in internet sites that allow to search for InChI codes (name/key). > In addition I am interested in recent publications regarding usage of InChI to locate molecules in internet databases. > Any feedback regarding the topic is appreciated. > Regards > HansH> > > -- Sebastian Rohrer AK Baumann - Molecular Modelling Group Institute of Pharmaceutical Chemistry Braunschweig University of Technology Beethovenstr. 55 38106 Braunschweig Germany Phone: +49-531-3912797 From owner-chemistry@ccl.net Fri Jan 18 04:08:00 2008 From: "Ramachandrann chelat rcchelat**rediffmail.com" To: CCL Subject: CCL: Molpro error due to memory problems Message-Id: <-36067-080117105136-14721-zbt0gDvjpDKE5NIRfk+6cQ]![server.ccl.net> X-Original-From: "Ramachandrann chelat" Date: Thu, 17 Jan 2008 10:51:32 -0500 Sent to CCL by: "Ramachandrann chelat" [rcchelat###rediffmail.com] Dear CCL Friends, I submitted one molpro job and it got terminated with the following error Contracted 2-electron integrals neglected if value below 1.0D-11 AO integral compression algorithm 1 Integral accuracy 1.0D-11 57358.156 MB (compressed) written to integral file ( 16.4%) Node minimum: 28517.597 MB, node maximum: 28840.559 MB NOT ENOUGH MEMORY IN SUBROUTINE AOSORT. GA ERROR fehler on processor 0 ********************** I have submitted the parallel molpro job with the following script file #!/bin/bash # [*] wall_clock_limit=24:00:00 # [*] job_type = parallel # [*] resources = ConsumableCpus(1) ConsumableMemory(1000 mb) # [*] network.MPI_LAPI = css0,shared,us # [*] total_tasks=2 # [*] output = example.log # [*] error = job.err # [*] shell = /bin/bash # [*] queue and the input file has the following section ! $Revision: 2006.0$ ***,big system memory,50,M geomtyp=xyz where I have to modify so that the job will run without any trouble? Thanking you, Ramachandran From owner-chemistry@ccl.net Fri Jan 18 07:30:00 2008 From: "Grant Hill hilljg]^[cardiff.ac.uk" To: CCL Subject: CCL: Molpro error due to memory problems Message-Id: <-36068-080118072533-29756-LcGpFIc45uGYSkfShCiqtw-.-server.ccl.net> X-Original-From: Grant Hill Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Fri, 18 Jan 2008 11:05:33 +0000 Mime-Version: 1.0 (Apple Message framework v915) Sent to CCL by: Grant Hill [hilljg^-^cardiff.ac.uk] On 17 Jan 2008, at 15:51, Ramachandrann chelat rcchelat**rediffmail.com wrote: > where I have to modify so that the job will run without any trouble? Your job appears to be running out of RAM, which you can adjust on the following line of your input file: > memory,50,M It's hard to know what a sensible amount of mem would be here without further details, but it's worth bearing in mind that it is measured in mwords, not mbytes. There is a specific molpro-users list, which may be a better place to seek further help. http://www.molpro.net/molpro-user/?portal=user&choice=User+mailing+list HTH, Grant From owner-chemistry@ccl.net Fri Jan 18 08:11:01 2008 From: "Joe Corkery jcorkery[A]eyesopen.com" To: CCL Subject: CCL: Viewing question Message-Id: <-36069-080117160653-24113-AE8wisDk/WWA1+psRDEaTA[-]server.ccl.net> X-Original-From: Joe Corkery Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 17 Jan 2008 14:06:14 -0500 MIME-Version: 1.0 Sent to CCL by: Joe Corkery [jcorkery:_:eyesopen.com] Hi Richard, VIDA from OpenEye Scientific Software (free for non-commercial use) is an excellent solution to your problem and was originally designed to handle problems such as this. VIDA even offers a one-step docking view for quick preparation of scenes just as you described. VIDA runs on Windows, Linux, and Mac OS X. Publication quality images can be created and printed from within VIDA as well as being able to export to POV-Ray if desired. An entire session can be saved out to a single file for continued work later or for easy sharing (files are small enough for email or web posting). Furthermore, OpenEye also offers Vivant which is an Active-X component which can be embedded in webpages or PowerPoint presentations for interactive viewing of your VIDA sessions during presentations. An academic license can be requested here: http://www.eyesopen.com/forms/academic_license_app.php Best of luck to you, Joe Corkery -- Joseph Corkery, M.D. Principal Developer OpenEye Scientific Software, Inc. 222 Third Street, Suite 3120 Cambridge, MA 02142 T: 505-473-7385 x76 F: 617-374-6575 From owner-chemistry@ccl.net Fri Jan 18 09:20:00 2008 From: "ramachandran chelat rcchelat a rediffmail.com" To: CCL Subject: CCL:G: Gaussian'98 Message-Id: <-36070-080118044918-10550-WAblihHHRp0J61iRYD+s6w- -server.ccl.net> X-Original-From: "ramachandran chelat" Content-type: multipart/alternative; boundary="Next_1200645978---0-202.54.124.131-18660" Date: 18 Jan 2008 08:46:18 -0000 MIME-Version: 1.0 Sent to CCL by: "ramachandran chelat" [rcchelat-#-rediffmail.com] This is a multipart mime message --Next_1200645978---0-202.54.124.131-18660 Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hai,=0AAs far as I know 32 bit gaussian version has limitation of total f= ile size, irrespective of you have free space or not.=0AIf t it is 64 bit v= ersion it should not be a problem, you can use as much as possible.=0AI had= a similar problem for a long time till we buy a 64 for bit version=0A=0A= =0A=0A=0AOn Fri, 18 Jan 2008 Gunes Bender gbender.wisc.edu wrote :=0A>=0A>S= ent to CCL by: "Gunes Bender" [gbender{=3D}wisc.edu]=0A>I am trying to do = QCISD(T) level calculations on a molecule about 20 atoms big using Gaussian= '98 on a linux platform. I tried creating extra scr and rwf files and speci= fying their sizes; so, I try to use many 240MW big files for the calculatio= n to use. My question is: Gaussian seems to read only the first 12 files, e= ven when I try to make it use more files than that. Does anyone know why Ga= ussian does this? And second of all, I am always running out of space. Does= anyone know any other tricks to do QCISD(T) calculations on fairly large m= olecules?=0A>Any information or help would be much appreciated.=0A>Thank yo= u,=0A>Gunes=0A>=0A>=0A>=0A>-=3D This is automatically added to each message= by the mailing script =3D-=0A>To recover the email address of the author o= f the message, please change=0A>the strange characters on the top line to t= he === sign. You can also=0A>look up the X-Original-From: line in the mail he= ader.=0A>=0A=0A> htt= p://www.ccl.net/cgi-bin/ccl/send_ccl_message=0A>=0A>E-mail to administrator= s: CHEMISTRY-REQUEST===ccl.net or use=0A> http://www.ccl.net/cgi-bin/cc= l/send_ccl_message=0A>=0A>Subscribe/Unsubscribe:=0A> http://www.ccl.n= et/chemistry/sub_unsub.shtml=0A>=0A>Before posting, check wait time at: htt= p://www.ccl.net=0A>=0A>Job: http://www.ccl.net/jobs=0A>Conferences: http://= server.ccl.net/chemistry/announcements/conferences/=0A>=0A>Search Messages:= http://www.ccl.net/htdig (login: ccl, Password: search)=0A>=0A>If your ma= il bounces from CCL with 5.7.1 error, check:=0A> http://www.ccl.net/s= pammers.txt=0A>=0A>RTFI: http://www.ccl.net/chemistry/aboutccl/instructions= /=0A>=0A>=0A=0A=0ARamachandran Chelat,=0D=0ADept. of Chemistry,=0D=0AIIT Ka= npur=0D=0AKanpur -208016=0D=0APh: +91-512-2597367=0D=0A=0D=0Ahttp://home.ii= tk.ac.in/~ramcn/ --Next_1200645978---0-202.54.124.131-18660 Content-type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline

=0A  Hai,
=0AAs far as I know 32 bit gaussian version has limita= tion of total file size, irrespective of you have free space or not.
=0A= If t it is 64 bit version it should not be a problem, you can use as much a= s possible.
=0AI had a similar problem for a long time till we buy a 64 = for bit version
=0A
=0A
=0A
=0A
=0AOn Fri, 18 Jan 2008 Gunes= Bender gbender.wisc.edu wrote :
=0A>
=0A>Sent to CCL by: "= ;Gunes  Bender" [gbender{=3D}wisc.edu]
=0A>I am trying to d= o QCISD(T) level calculations on a molecule about 20 atoms big using Gaussi= an'98 on a linux platform. I tried creating extra scr and rwf files and spe= cifying their sizes; so, I try to use many 240MW big files for the calculat= ion to use. My question is: Gaussian seems to read only the first 12 files,= even when I try to make it use more files than that. Does anyone know why = Gaussian does this? And second of all, I am always running out of space. Do= es anyone know any other tricks to do QCISD(T) calculations on fairly large= molecules?
=0A>Any information or help would be much appreciated.=0A>Thank you,
=0A>Gunes
=0A>
=0A>
=0A>
=0A&= gt;-=3D This is automatically added to each message by the mailing script = =3D-
=0A>To recover the email address of the author of the message, p= lease change
=0A>the strange characters on the top line to the === sign= . You can also
=0A>look up the X-Original-From: line in the mail head= er.
=0A>
=0A>=0A>      http://www.ccl.net/cgi-bin/ccl/send_ccl_mess= age
=0A>
=0A>E-mail to administrators: CHEMISTRY-REQUEST===ccl.ne= t or use
=0A>      http://www.ccl.net/cgi-bin/ccl/sen= d_ccl_message
=0A>
=0A>Subscribe/Unsubscribe:
=0A>  =    
=0A>
= =0A>
=0A>=0A>Job: http://www.ccl.net/jobs
=0A>Conferences: http://server.c= cl.net/chemistry/announcements/conferences/
=0A>
=0A>Search Mes= sages: http://www.ccl.net/htdig  (login: ccl, Password: search)
=0A= >
=0A>
= =0A>     
=0A>
= =0A>
=0A>=
=0A>
=0A=0A

=0A=0A=0ARamachandran Chelat,=0D
=0ADept. of&nb= sp;Chemistry,=0D
=0AIIT Kanpur=0D
=0AKanpur -208016=0D
=0APh: +91-= 512-2597367=0D
=0A=0D
=0Ahttp://home.iitk.ac.in/~ramcn/

=0A3D'Simply= --Next_1200645978---0-202.54.124.131-18660-- From owner-chemistry@ccl.net Fri Jan 18 09:55:00 2008 From: "Ioana Sovago isovago a chem.ubbcluj.ro" To: CCL Subject: CCL: ccl subsctibers Message-Id: <-36071-080118091846-19765-s7+WoDWt1ZmoLwJORpTQSw * server.ccl.net> X-Original-From: "Ioana Sovago" Date: Fri, 18 Jan 2008 09:18:43 -0500 Sent to CCL by: "Ioana Sovago" [isovago**chem.ubbcluj.ro] My name is Sovago Ioana and I want an acount for the ccl site. I am a Phd student at the chemistry faculty of Babes Bolyai University Cluj Napoca, Roumania. Thanks From owner-chemistry@ccl.net Fri Jan 18 11:36:01 2008 From: "William F. Polik polik[*]hope.edu" To: CCL Subject: CCL: Molpro error due to memory problems Message-Id: <-36072-080118102429-25035-XJqhZl2QNAfWPRksmtnE9g ~ server.ccl.net> X-Original-From: "William F. Polik" Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Fri, 18 Jan 2008 08:31:43 -0500 Mime-Version: 1.0 Sent to CCL by: "William F. Polik" [polik,hope.edu] Ramachandran, It appears that while you have 1000MB (= 1GB) available on your system, you have only allocated 50MW (= 8*50MB = 400MB) to your job. Try increasing the memory in your "memory,50,M" line. Will Polik At 10:51 AM 1/17/2008, "Ramachandrann chelat" [rcchelat###rediffmail.com] wrote: >I have submitted the parallel molpro job with the following script file >#!/bin/bash ># -#- wall_clock_limit=24:00:00 ># -#- job_type = parallel ># -#- resources = ConsumableCpus(1) ConsumableMemory(1000 mb) > >... > >and the input file has the following section >! $Revision: 2006.0$ >***,big system >memory,50,M >geomtyp=xyz From owner-chemistry@ccl.net Fri Jan 18 14:27:00 2008 From: "zhendong zhao zzhao!A!olemiss.edu" To: CCL Subject: CCL:G: fchk file of different gaussian version Message-Id: <-36073-080118121801-30952-lNCaeN/Gjrxn1q7of8ZvEw{=}server.ccl.net> X-Original-From: zhendong zhao Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Fri, 18 Jan 2008 10:46:28 -0600 Mime-Version: 1.0 Sent to CCL by: zhendong zhao [zzhao!A!olemiss.edu] Dear cclers, I sent an email to gaussian tech support, but by now I got no response > from them, I guess they are unhappy to answer such a question. Now I sent an email to ccl list asking for help. I have a question about fchk file of the different version G94, G98, and G03. Is the format exactly same, especially for the part, Alpha MO coefficients in the fchk file? If different, does there exist tools to convert each other? Appreciate your help. zhendong zhao OLE MISS From owner-chemistry@ccl.net Fri Jan 18 16:46:01 2008 From: "zhendong zhao zzhao,+,olemiss.edu" To: CCL Subject: CCL:G: fchk file of different gaussian version Message-Id: <-36074-080118163203-14332-jpOf5g7kpubsofrvT1EjdQ]=[server.ccl.net> X-Original-From: zhendong zhao Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Fri, 18 Jan 2008 15:29:57 -0600 Mime-Version: 1.0 Sent to CCL by: zhendong zhao [zzhao+*+olemiss.edu] CCLers, I got an email from Gaussian tech support, they tried to answer my question. I would like to say thanks to gaussian tech support. If you have any idea about the difference of fchk file, please do answer me the question, appreciate your help. Best regards, zhendong zhao OLE MISS On Fri, 18 Jan 2008 10:46:28 -0600 "zhendong zhao zzhao!A!olemiss.edu" wrote: > > Sent to CCL by: zhendong zhao [zzhao!A!olemiss.edu] > Dear cclers, > I sent an email to gaussian tech support, but by now I got no response > > from them, I guess they are unhappy to answer such a question. Now I > sent an email to ccl list asking for help. > > I have a question about fchk file of the different version G94, G98, > and G03. Is the format exactly same, especially for the part, Alpha MO > coefficients in the fchk file? If different, does there exist tools to > convert each other? > > Appreciate your help. > > zhendong zhao > OLE MISS > > > > -= This is automatically added to each message by the mailing script > =- To recover the email address of the author of the message, please > change the strange characters on the top line to the -.- sign. You can > also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> >