From owner-chemistry@ccl.net Wed Oct 5 11:18:00 2005 From: "Joe Harriman j.harriman]-[unb.ca" To: CCL Subject: CCL: W:Connelly Surface of Cavities Message-Id: <-29491-051005103051-23622-w4tUXVfBNyCTL+PbHV8l4A%server.ccl.net> X-Original-From: Joe Harriman Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Wed, 5 Oct 2005 10:50:55 -0300 Mime-Version: 1.0 (Apple Message framework v734) Sent to CCL by: Joe Harriman [j.harriman/a\unb.ca] Hi Don, The Molecular Operating Environment (MOE) developed by CCG can generate surfaces over a group of any selected atoms. -Joe On 4-Oct-05, at 10:44 PM, Donald James Keidel keided01() student.ucr.edu wrote: > > Sent to CCL by: "Donald James Keidel" [keided01^_^student.ucr.edu] > I am looking for a program, free or not, that can fill in the gaps > of cavities in proteins with a connelly surface. As i understand > it now programs can generate a connelly surface over the protein > atoms. I want to be able to visualize the cavities in proteins. > Thank you in advance for all replies. > > Don > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > > From owner-chemistry@ccl.net Wed Oct 5 11:53:00 2005 From: "Terry Frankcombe T.Frankcombe : chem.leidenuniv.nl" To: CCL Subject: CCL: W:help with job termination Message-Id: <-29492-051005050938-3135-3Nj2zZwvCfCCfgRczsR8PQ%%server.ccl.net> X-Original-From: Terry Frankcombe Content-Type: text/plain; charset=us-ascii Date: Wed, 05 Oct 2005 11:09:19 +0200 Mime-Version: 1.0 Sent to CCL by: Terry Frankcombe [T.Frankcombe],[chem.leidenuniv.nl] > > Sent to CCL by: "Ayorinde S Hassan" [ayo_hassan]|[yahoo.com] > I would like some help with a job am running. The job terminates with the fol lowing message: "The electronic state of the initial guess is 4-A. > of initial guess= 3.7500 > Defaulting to unpruned grid for atomic number 66. > Gradient too large for Newton-Raphson or scaled steepest descent -- > use steepest descent instead. > Erroneous write. write 23584 instead of 80000. > fd = 5" I would appreciate any help or suggestion . Ayorinde Assuming you're talking about Gaussian (a rather big assumption), this error typically means you are beyond your scratch capabilities. So either your scratch space is full/broken or your RWF is bigger than the OS limit (often 2 or 16 GB). In the latter case try MaxDisk or splitting your RWF into size-limited chunks. -- Dr Terry Frankcombe LIC / Theoretical Chemistry University of Leiden Postbus 9502, 2300 RA Leiden, The Netherlands Ph. +31 71 527 4533 Fax +31 71 527 4397 From owner-chemistry@ccl.net Wed Oct 5 12:28:01 2005 From: "Luis M Simn luissimonrubio*_*hotmail.com" To: CCL Subject: CCL: W:gaussian03 vs. schrodinger jaguar packages Message-Id: <-29493-051005060429-8237-1bWQpb8zKvQ2ihZTvsy3JQ;;server.ccl.net> X-Original-From: "Luis M Simn" Sent to CCL by: "Luis M Simn" [luissimonrubio .. hotmail.com] Dear all: I dont want to start a "religous" war, but can anyone explain me which are the advantages of gaussian03 and jaguar (including relating products). Which allows faster single point, optimization, hessian calculation, etc? which is more complete? Which allows to use third party software for visualization or input preparing? What about the prices? I have found academic licenses prices for gaussian03, but for jaguar you need to contact a sale agent (thats something that I would not lide to do now) thanks to all: Luis From owner-chemistry@ccl.net Wed Oct 5 13:03:00 2005 From: "Ivanciuc, Ovidiu I. oiivanci+*+utmb.edu" To: CCL Subject: CCL: Connolly Surface of Cavities Message-Id: <-29494-051005112406-32071-Kv84p4o6jJUcmf3KWxwJqg*server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="Windows-1252" Date: Wed, 5 Oct 2005 10:23:59 -0500 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci]^[utmb.edu] >>I am looking for a program, free or not, >> that can fill in the gaps of cavities in proteins CASTp, http://cast.engr.uic.edu/cast/ Surface Racer, http://monte.biochem.wisc.edu/~tsodikov/surface.html Regards, Ovidiu ********************************* Ovidiu Ivanciuc Sealy Center for Structural Biology, Department of Human Biological Chemistry & Genetics, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-1157 USA From owner-chemistry@ccl.net Wed Oct 5 13:37:00 2005 From: "Jose Gascon jose.gascon..yale.edu" To: CCL Subject: CCL: DELPHI dielectric boundary condition Message-Id: <-29495-051005131126-32220-Q/x//ou3m1x3ye/A5+XEXQ[A]server.ccl.net> X-Original-From: Jose Gascon Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 05 Oct 2005 12:12:25 -0400 MIME-Version: 1.0 Sent to CCL by: Jose Gascon [jose.gascon]-[yale.edu] Dear all Does anyone know what is the default for dielectric boundary conditions in DELPHI? As I understand there could be two possibilities 1) abrupt dielectrict surfaces or 2) spline smoothed surfaces. Thanks, Regards, Jose. -- Jose A. Gascon - Postdoctoral Associate Department of Chemistry - (203)432-5911; jose.gascon-.-yale.edu Yale University P.O. Box 208107 New Haven, CT 06520-8107. From owner-chemistry@ccl.net Wed Oct 5 14:33:00 2005 From: "Andrea Carotti and.carotti * farmchim.uniba.it" To: CCL Subject: CCL: W:Connelly Surface of Cavities Message-Id: <-29496-051005131324-32480-RRXW0uduH6eNa0DORipOfg---server.ccl.net> X-Original-From: "Andrea Carotti" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=response Date: Wed, 5 Oct 2005 17:53:29 +0200 MIME-Version: 1.0 Sent to CCL by: "Andrea Carotti" [and.carotti!A!farmchim.uniba.it] Hi Don, I think that here you'll find what you are looking for: http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html In my opinion it's a wonderfull program, ease to use and very usefull. Hope this help Andrea ----- Original Message ----- > From: "Joe Harriman j.harriman]-[unb.ca" To: "Carotti, Andrea " Sent: Wednesday, October 05, 2005 3:50 PM Subject: CCL: W:Connelly Surface of Cavities > > Sent to CCL by: Joe Harriman [j.harriman/a\unb.ca] > Hi Don, > > The Molecular Operating Environment (MOE) developed by CCG can > generate surfaces over a group of any selected atoms. > > -Joe > > On 4-Oct-05, at 10:44 PM, Donald James Keidel keided01() > student.ucr.edu wrote: > >> >> Sent to CCL by: "Donald James Keidel" [keided01^_^student.ucr.edu] >> I am looking for a program, free or not, that can fill in the gaps >> of cavities in proteins with a connelly surface. As i understand >> it now programs can generate a connelly surface over the protein >> atoms. I want to be able to visualize the cavities in proteins. >> Thank you in advance for all replies. >> >> Don >> >> >> >> -= This is automatically added to each message by the mailing >> script =- >> To recover the email address of the author of the message, please >> change> >> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- >> +-+-+> > From owner-chemistry@ccl.net Wed Oct 5 15:08:00 2005 From: "Steve Bowlus chezbowlus||goldrush.com" To: CCL Subject: CCL: Open source contributions by pharma. Message-Id: <-29497-051005141230-4284-P0Tqm9WwJnab0pNH8tn+Ew]-[server.ccl.net> X-Original-From: Steve Bowlus Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 05 Oct 2005 11:12:08 -0700 MIME-Version: 1.0 Sent to CCL by: Steve Bowlus [chezbowlus^-^goldrush.com] The Verloop STERIMOL program is available from QCPE (wrt the initial thread, Verloop developed and distributed the program while at Duphar; I ported it to the PC while at Novartis Agro). AFAIK all other programs including STERIMOL parameters are derivatives of Verloop's program. This includes a Sybyl SPL contributed by a worker then at Dow Agroscience. I believe the distribution package of the port includes Verloop's original code for the VAX, if you want to slick things up. sb CCL wrote: > Sent to CCL by: Rajarshi Guha [rxg218^^psu.edu] > > --Replace strange characters with the "at" sign to recover email address--. > > On Wed, 2005-09-28 at 16:46 -0700, CCL wrote: > >>Sent to CCL by: "Peter Spiro" [spiro(a)renovis.com] >> > > >>On the subject of cheminformatics applications such as descriptor >>calculation, conformational search, QSAR, etc, I'd be interested to >>know people's recommendations for open source/free/cheap software in >>this area. Is there anything that comes close to, say, MOE? > > > For descriptor calculations JOElib is nice - there was a post on this > list sometime back summarizing free/opensource descriptor calculation > software. > > For QSAR modeling a good opensource program is R > > As for combining descriptor calculation & modeling you have commercial > software, such as MOE and others. On the free/opensource side, PowerMV > (http://www.niss.org/PowerMV/) is one possibility (which actually uses R > as the backend). > > ------------------------------------------------------------------- > Rajarshi Guha > GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE > ------------------------------------------------------------------- > 667: > The neighbor of the beast.> > Job advertising: http://www.ccl.net/jobs > > If your mail bounces from CCL with 5.7.1 error check:> > > > > From owner-chemistry@ccl.net Wed Oct 5 16:20:00 2005 From: "David Santos Carballal spectrum_dav_._operamail.com" To: CCL Subject: CCL: Box of solvent Message-Id: <-29498-051005151639-13309-mPaOqJp7fVO88Aub2xF8Lw;;server.ccl.net> X-Original-From: "David Santos Carballal" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 05 Oct 2005 20:16:31 +0100 MIME-Version: 1.0 Sent to CCL by: "David Santos Carballal" [spectrum_dav{}operamail.com] I am trying to make a dynamic with a box of solvent in TINKER. How can I apply periodic boundary conditions? David Santos Carballal -- _______________________________________________ Surf the Web in a faster, safer and easier way: Download Opera 8 at http://www.opera.com Powered by Outblaze From owner-chemistry@ccl.net Wed Oct 5 16:56:00 2005 From: "Gustavo L.C. Moura gustavo[-]mercury.chem.pitt.edu" To: CCL Subject: CCL: W:Program for reading MOPAC output Message-Id: <-29499-051005165457-23475-UP5Mfr8K7lAv18J3vP2grw%server.ccl.net> X-Original-From: "Gustavo L.C. Moura" Sent to CCL by: "Gustavo L.C. Moura" [gustavo~!~mercury.chem.pitt.edu] Dear CCL readers, I have a large number of molecules that I have optimized using the MOPAC program. I would like to know if there is a graphical program that can read the MOPAC output, draw the molecule on the screen and provide an easy way of showing the charges over each one of the atoms. The program could either show the charges as a label over the atoms or as a table beside the drawn molecule. I am really looking for a free for academia program, but any suggestions are welcome. The program should be for Windows or Linux operating systems. Thank you very much in advance for your help. Sincerely yours, Gustavo L.C. Moura From owner-chemistry@ccl.net Wed Oct 5 19:31:00 2005 From: "Wayne Steinmetz WES04747]=[pomona.edu" To: CCL Subject: CCL: W:Program for reading MOPAC output Message-Id: <-29500-051005191317-32592-L6/squ2cTO7JKhqREP/lDA||server.ccl.net> X-Original-From: "Wayne Steinmetz" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 5 Oct 2005 16:12:05 -0700 MIME-Version: 1.0 Sent to CCL by: "Wayne Steinmetz" [WES04747###pomona.edu] Wonderful tools are not free. SYBYL which has an excellent molecular spreadsheet includes MOPAC and the tools to read MOPC files. Wayne E. Steinmetz Carnegie Professor of Chemistry Woodbadge Course Director Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-707-7726 Email: wsteinmetz|pomona.edu WWW: pages.pomona.edu/~wsteinmetz -----Original Message----- > From: owner-chemistry|ccl.net [mailto:owner-chemistry|ccl.net] Sent: Wednesday, October 05, 2005 12:58 PM To: Wayne Steinmetz Subject: CCL: W:Program for reading MOPAC output Sent to CCL by: "Gustavo L.C. Moura" [gustavo~!~mercury.chem.pitt.edu] Dear CCL readers, I have a large number of molecules that I have optimized using the MOPAC program. I would like to know if there is a graphical program that can read the MOPAC output, draw the molecule on the screen and provide an easy way of showing the charges over each one of the atoms. The program could either show the charges as a label over the atoms or as a table beside the drawn molecule. I am really looking for a free for academia program, but any suggestions are welcome. The program should be for Windows or Linux operating systems. Thank you very much in advance for your help. Sincerely yours, Gustavo L.C. Mourahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------------------------------------------------------------- This message has been scanned by Postini anti-virus software. From owner-chemistry@ccl.net Wed Oct 5 20:06:00 2005 From: "Sanyasi Sitha sitha__bc.edu" To: CCL Subject: CCL: Reading the GAMESS outfile Message-Id: <-29501-051005175108-24938-ein0qKRl9bt+84V4SySLVw=server.ccl.net> X-Original-From: Sanyasi Sitha Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-1" Date: Wed, 05 Oct 2005 16:50:56 -0400 MIME-Version: 1.0 Sent to CCL by: Sanyasi Sitha [sitha|*|bc.edu] Hi I am a student from Boston college. I am using the GAMESS program to do optimization and property calculations. I tried to visualize my GAMESS output results with some of the freely available visualization softwares like Facio, gOpenMol----but till now I was not able to find a suitable one. I will be grateful if some one can suggest me a suitable program to visualize my GAMESS out file. thanking you Name: Sanyasi Sitha Email: sitha[A]bc.edu From owner-chemistry@ccl.net Wed Oct 5 20:41:00 2005 From: "Aaron Deskins ndeskins---purdue.edu" To: CCL Subject: CCL: What keeps a molecule adsorbed? Message-Id: <-29502-051005182606-27911-7h+0ITqyyx1mi5cFVsm06A#%#server.ccl.net> X-Original-From: Aaron Deskins Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Wed, 05 Oct 2005 17:26:00 -0500 MIME-Version: 1.0 Sent to CCL by: Aaron Deskins [ndeskins|,|purdue.edu] Mariusz Sterzel msterzel(a)buffalo.edu wrote: > > Sent to CCL by: Mariusz Sterzel [msterzel^_^buffalo.edu] > Dear Noel, > > Following Ruedenberg, the simple answer is electrons kinetic energy. > For more details look at K. Ruedenberg, Reviews of Modern Physics, > 34(2):326-376, (1962) and M.S. Gordon, J.H.Jensen, Theoretical > Chemistry Accounts, 103:248-251, (2000) > > There are excellent articles and quite informative. Any discussion of the fundamental concept of bonding is useful for better chemistry understanding. Therefore, I would like to solicit any other similar articles, books, etc. that discuss bonding and the like. Thank you, Aaron Deskins Purdue University From owner-chemistry@ccl.net Wed Oct 5 21:16:00 2005 From: "cesar mujica cesarmujica/./gmail.com" To: CCL Subject: CCL: W:Program for reading MOPAC output Message-Id: <-29503-051005192100-779-LXlrk5Ui6B4hjutnzkMEvg:server.ccl.net> X-Original-From: cesar mujica Content-Type: multipart/alternative; boundary="----=_Part_9624_26921107.1128550692790" Date: Wed, 5 Oct 2005 17:18:12 -0500 MIME-Version: 1.0 Sent to CCL by: cesar mujica [cesarmujica+*+gmail.com] ------=_Part_9624_26921107.1128550692790 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear Gustavo, Exist a free software namely MOLDEN and your can download in http://www.cmbi.ru.nl/molden/molden.html I hope that this program are useful for you. Best regards, Cesar Mujica cesarmujica(!)gmail.com Chemistry Department Universidad del Valle On 10/5/05, Gustavo L.C. Moura gustavo[-]mercury.chem.pitt.edu < owner-chemistry(!)ccl.net> wrote: > > > Sent to CCL by: "Gustavo L.C. Moura" [gustavo~!~mercury.chem.pitt.edu] > Dear CCL readers, > I have a large number of molecules that I have optimized using the MOPAC > program. I would like to know if there is a graphical program that can re= ad > the MOPAC output, draw the molecule on the screen and provide an easy way= of > showing the charges over each one of the atoms. The program could either > show the charges as a label over the atoms or as a table beside the drawn > molecule. > I am really looking for a free for academia program, but any suggestions > are welcome. The program should be for Windows or Linux operating systems= . > Thank you very much in advance for your help. > Sincerely yours, > Gustavo L.C. Moura > > ------=_Part_9624_26921107.1128550692790 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Dear Gustavo,
 
Exist a free software namely MOLDEN and your can download in
 
I hope that this program are useful for you.
 
Best regards,
 
Cesar Mujica
cesarmujica(!)gmail.com
Chemistry Department
Universidad del Valle


 
On 10/5/05, = Gustavo L.C. Moura gustavo[-]mercury.chem.pitt.edu <owner-chemistry(!)ccl.net> wrote:

Sent to CCL by: "Gustav= o L.C. Moura" [gustavo~!~mercury.chem.pitt.edu]
Dear CCL readers,     I have a large number of molecules that I have opti= mized using the MOPAC program. I would like to know if there is a graphical= program that can read the MOPAC output, draw the molecule on the screen an= d provide an easy way of showing the charges over each one of the atoms. Th= e program could either show the charges as a label over the atoms or as a t= able beside the drawn molecule.
    I am really looking for a free for academia pro= gram, but any suggestions are welcome. The program should be for Windows or= Linux operating systems.
    Thank you very much in= advance for your help.
    Sincerely yours,
            = ;            &n= bsp;      Gustavo L.C. Moura

<= /div> ------=_Part_9624_26921107.1128550692790-- From owner-chemistry@ccl.net Wed Oct 5 21:50:01 2005 From: "William F. Polik polik]=[hope.edu" To: CCL Subject: CCL: W:Program for reading MOPAC output Message-Id: <-29504-051005213211-30626-70BBs2rRWWfr8XfrM1JYMw[#]server.ccl.net> X-Original-From: "William F. Polik" Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Wed, 05 Oct 2005 20:46:36 -0400 Mime-Version: 1.0 Sent to CCL by: "William F. Polik" [polik%hope.edu] Gustavo, At 05:00 PM 10/5/2005, you wrote: > I have a large number of molecules that I have optimized using > the MOPAC program. I would like to know if there is a graphical > program that can read the MOPAC output, draw the molecule on the > screen and provide an easy way of showing the charges over each one > of the atoms. The program could either show the charges as a label > over the atoms or as a table beside the drawn molecule. > I am really looking for a free for academia program, but any > suggestions are welcome. The program should be for Windows or Linux > operating systems. > Thank you very much in advance for your help. WebMO,(www.webmo.net) has the capability to import files and graphically display the results, including partial charges. WebMO is free and installs on any unix server, including Linux. Since WebMO is web-based, you can then access it from almost any web-browser (Windows, Linux, OS X). Before installing WebMO on your own, try out the Working Demo at www.webmo.net/demo After logging in as username="guest" and password="guest", choose New Job: Import Job. Give the job a name, choose MOPAC file type, and browse to your local output file. Click Import Job and WebMO will upload your output file and add it to its list of jobs in Job Manager. Click on the job name to view your results graphically. Of course, WebMO is designed to provide a comprehensive web-based interface for building, submitting, and viewing computational chemistry jobs. But it also allows the viewing of previously computed jobs as you have requested. And its free! Will Polik ================================ Dr. William F. Polik Hofma Professor of Chemistry Department of Chemistry Hope College 35 East 12th Street Holland, MI 49422-9000 USA polik.:.hope.edu http://www.chem.hope.edu/~polik tel: (616) 395-7639 fax: (616) 395-7118 ================================ From owner-chemistry@ccl.net Wed Oct 5 22:36:00 2005 From: "sasha lesyk;;berkeley.edu" To: CCL Subject: CCL: Reading the GAMESS outfile Message-Id: <-29505-051005214224-3658-p6aXGvYBHq/1KgFeroNVtA a server.ccl.net> X-Original-From: sasha Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 05 Oct 2005 17:39:13 -0700 Mime-Version: 1.0 Sent to CCL by: sasha [lesyk+*+berkeley.edu] Try using molden, http://www.cmbi.ru.nl/molden/molden.html regards, Sasha On Wed, 2005-10-05 at 16:50 -0400, Sanyasi Sitha sitha__bc.edu wrote: > Sent to CCL by: Sanyasi Sitha [sitha|*|bc.edu] > Hi > I am a student from Boston college. I am using the GAMESS program to do > optimization and property calculations. I tried to visualize my GAMESS > output results with some of the freely available visualization softwares > like Facio, gOpenMol----but till now I was not able to find a suitable > one. I will be grateful if some one can suggest me a suitable program to > visualize my GAMESS out file. > > thanking you > > Name: Sanyasi Sitha > Email: sitha=bc.edu> > >