From chemistry-request@server.ccl.net Fri Dec 7 04:32:46 2001 Received: from mailbox.univie.ac.at ([131.130.1.27]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB79Wii27987 for ; Fri, 7 Dec 2001 04:32:45 -0500 Received: from univie.ac.at (IDENT:WT9ewHtxhovXW2aNgNkVijtx6l1YZVod@ganges.itc.univie.ac.at [131.130.39.6]) by mailbox.univie.ac.at (8.11.2/8.11.2) with ESMTP id fB79WTu96766 for ; Fri, 7 Dec 2001 10:32:29 +0100 Sender: silmar@mailbox.univie.ac.at Message-ID: <3C108A5B.B7219EC4@univie.ac.at> Date: Fri, 07 Dec 2001 10:22:35 +0100 From: Silmar Andrade do Monte Organization: Institute for theoretical chemistry X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.9-13 i586) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re:CISD error Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Hua-Jun, I would suggest to decrease the number of MO's used for correlation, using the RW(read-window) option(CISD=RW). You could start with a small number of MO's and then increase it in steps. Using this approach you can find out if the problem is due to the large number os MO's and you can also have a convergence of the property that you want to calculate without using so many orbitals, saving computational time. Regards, Silmar From chemistry-request@server.ccl.net Fri Dec 7 05:08:01 2001 Received: from relay1.softcomca.com ([168.144.1.67]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB7A7wi28771 for ; Fri, 7 Dec 2001 05:08:01 -0500 Received: from m2w054 ([168.144.108.54]) by relay1.softcomca.com with Microsoft SMTPSVC(5.0.2195.3779); Fri, 7 Dec 2001 05:07:45 -0500 X-Originating-IP: 202.185.72.119 X-URL: http://www.mail2web.com/ Subject: calculate/visualize electrostatic changes for protein-ligand Sender: "nepenthes@vplaces.net" From: "nepenthes@vplaces.net" Date: Fri, 7 Dec 2001 05:07:56 -0500 To: "chemistry@ccl.net" Reply-To: nepenthes@vplaces.net X-Priority: 3 X-MSMail-Priority: Normal MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Mailer: JMail 3.7.0 by Dimac (www.dimac.net) Message-ID: X-OriginalArrivalTime: 07 Dec 2001 10:07:45.0741 (UTC) FILETIME=[04573FD0:01C17F07] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-Printable to 8bit by server.ccl.net id fB7A81i28774 Dear CCLers, I'm trying to get a comparison of the changes in the electrostatic charges of a protein before and after docking a ligand It would be nice to get details of the changes and also a visual of the distribution of charges. I tried to use InsightII by merging the ligand and unbound protein together but the charges did not change at all (as seen by the output file of the charges etc). I'm quite sure there must be some changes when a ligand binds. I might be doing it wrong so I would be glad for any suggestions as to how I can perform this. I think Delphi can manage this but I would prefer to try with a free software if available. Thank you all for your time. Regards, Rowyna K. -------------------------------------------------------------------- mail2web - Check your email from the web at http://mail2web.com/ . From chemistry-request@server.ccl.net Fri Dec 7 06:17:33 2001 Received: from mserv.itpa.lt ([193.219.53.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB7BHUi30217 for ; Fri, 7 Dec 2001 06:17:30 -0500 Received: from localhost (tamulis@localhost) by mserv.itpa.lt (8.11.6/8.11.0) with ESMTP id fB7BHEZ48124; Fri, 7 Dec 2001 13:17:14 +0200 (EET) (envelope-from tamulis@itpa.lt) Date: Fri, 7 Dec 2001 13:17:14 +0200 (EET) From: Arvydas Tamulis To: "Prof.Dr.Stefan Grimme" cc: Subject: Re: CCL:Fwd: RHO-CI density In-Reply-To: <0112070946020U.04643@goofy1> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id fB7BHXi30218 Dear Professor Grimme and other CCL Colleagues, Thanks for your recommendation to use TDHF. I will do this in the case if it is possible to do this in Gaussian98. I understand that it is neccessary to chosse keywords by such a way: #P HF 6-311G TD(NStates=7,Root=2) Density=all Do it is true? My colleagues also sayed that TDHF exist in GAMESS-US. We will try also this opportunity. We started works for programming PBE potential that it is absent presently in G98. What it is your opinion about this potential? Maybe it is suitable for exact DFT-TD charge thansfer evaluations? Actually I need qualitative evaluations of charge transfer from different branches of supermolecules in different excited states: PhotoElectronDonor1 \_______ElectronAcceptor / PhotoElectronDonor2 Acctually I received that using DFT-TD B3PW91 during one set of excitations electron charge is going from PhotoDonor1 and during another one set of excitations electron is moving from another PhotoDonor2. Of course exist some mixing of states but in general the charge transfer it is as I described here and in my article that I have sent you some time ago. Of course, I need to describe all these charge transfers as much as possible exactly therefore your further advises are welcome. Thanking your in advance. With best regards, Arvydas Tamulis (www.itpa.lt/~tamulis/) ****************************************************************** On Fri, 7 Dec 2001, Prof.Dr.Stefan Grimme wrote: > Dear Dr. Tamulis, > I'm not answering your question but instead want to point > out that TDDFT is in general NOT suitable for the calculation > of charge transfer in excited states, at least with common > functionals currently in use. The reason is the wrong > asymtotic form of the DF potential which artificially lowers > CT states and which produces to much charge separation. > I strongly recommend to compare with TDHF if the > qualitative picture is consistent with that from TDDFT. > Best wishes > Stefan Grimme > _________________________________________________________ > Prof. Dr. Stefan Grimme > Organisch-Chemisches Institut (Abt. Theoretische Chemie) > Westfaelische Wilhelms-Universitaet, Corrensstrasse 40 > D-48149 Muenster, Tel (+49)-251-83 36512/33241/36515(Fax) > Email:grimmes@uni-muenster.de > http://www.uni-muenster.de/Chemie/OC/research/grimme/ > _________________________________________________________ > Positions available for carrying out doctoral or > postdoctoral studies in chemistry in Münster: > http://www.uni-muenster.de/Chemie/OC/positions/ > _________________________________________________________ > From chemistry-request@server.ccl.net Fri Dec 7 05:33:46 2001 Received: from relay.uni-heidelberg.de ([129.206.100.212]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB7AXji29345 for ; Fri, 7 Dec 2001 05:33:45 -0500 Received: from fubini.pci.uni-heidelberg.de (fubini.pci.uni-heidelberg.de [129.206.21.240]) by relay.uni-heidelberg.de (8.10.2+Sun/8.10.2) with ESMTP id fB7AXUa25889; Fri, 7 Dec 2001 11:33:31 +0100 (MET) Received: from euklid (euklid.pci.uni-heidelberg.de [129.206.21.104]) by fubini.pci.uni-heidelberg.de (8.11.0/8.11.0/SuSE Linux 8.11.0-0.4) with SMTP id fB7AXPd28381; Fri, 7 Dec 2001 11:33:25 +0100 X-Authentication-Warning: fubini.pci.uni-heidelberg.de: Host euklid.pci.uni-heidelberg.de [129.206.21.104] claimed to be euklid Content-Type: text/plain; charset="iso-8859-15" From: Bernd Schubert To: chemistry@ccl.net Subject: G98 Basis set warning -- chkbasis keyword Date: Fri, 7 Dec 2001 11:33:24 +0100 X-Mailer: KMail [version 1.2] Cc: help@gaussian.com MIME-Version: 1.0 Message-Id: <01120711332400.09987@euklid> Content-Transfer-Encoding: 8bit Hi, a few days before I tried to use the keyword chkbasis for the very first time using G98A7. But when I checked if the same basis set has read in, as I have used in the previous calculation, the output showed me that the basis set had terribly enlarged -- 145 basis functions for my molecule from the original DZP basis set (from http://www.emsl.pnl.gov:2080/forms/basisform.html) had increased to 491 basis functions for the same molecule. Of course, the calculation took much more time than it should have using the DZP basis set (I stopped it after 5h and used the original basis set again -- calculation time about 10 min) Since I didn't find anything in the archives about this special 'feature', I just wanted to inform you about it -- and perhaps the people from Gaussian Inc. can give a statement about it. -- Bernd Schubert Physikalisch Chemisches Institut Abt. Theoretische Chemie INF 229, 69120 Heidelberg Tel.: 06221/54-5210 e-mail: bernd.schubert@tc.pci.uni-heidelberg.de From chemistry-request@server.ccl.net Fri Dec 7 08:58:45 2001 Received: from mail-c.bcc.ac.uk ([144.82.100.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB7Dwji01861 for ; Fri, 7 Dec 2001 08:58:45 -0500 Received: from dale.ri.ac.uk by mail-c.bcc.ac.uk with SMTP (Mailer) with ESMTP; Fri, 7 Dec 2001 13:58:30 +0000 Received: from ri.ac.uk (davy.ri.ac.uk) by dale.ri.ac.uk (Content Technologies SMTPRS 4.1.5) with SMTP id for ; Fri, 7 Dec 2001 13:57:32 +0000 Received: from tyndall.ri.ac.uk by ri.ac.uk (5.x/SMI-SVR4) id AA23372; Fri, 7 Dec 2001 13:58:28 GMT Received: from localhost by tyndall.ri.ac.uk (980427.SGI.8.8.8) id NAA93302; Fri, 7 Dec 2001 13:58:26 GMT Date: Fri, 7 Dec 2001 13:58:26 +0000 From: Naseem Ramsahye To: chemistry@ccl.net Subject: An ONIOM question Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am a Phd Student at the Royal Institution in London. I am using G98 to do some calcs on large zeolite clusters, using the ONIOM scheme. The scheme i'm using is ONIOM(B3LYP/6-31G**:AM1) However, in a couple of my calcs, I alway get the same error: Process number 1 did not complete successfully. Error termination via Lnk1e in /usr/local/opt/g98/l502.exe. This usually occurs after 166 cycles, and gives the UNIX error: pm_create: Arg list too long Could not create MLD: Not enough space Do you know what this is? I don't think I'm out of disk quota. I was wondering if it may be my system... I am treating the high level part at B3LYP (about 40 atoms), and the other part at AM1... I have successfully used this scheme before with a very similar system, in fact the only thing that's different here is that the system is slightly bigger. Also, I have usually treated the terminating hydrogen atoms as being fixed, and at the medium level. This time, four of the hydrogens are at the higher level, but still fixed. Would this cause a problem? I'd be grateful for any help you can give. Thanks for you help. Best Regards Naseem ------------------------------------------------------------------------ Naseem A. Ramsahye Research Student, DFRL Royal Institution of Great Britain, 21 Albemarle Street, LONDON W1S 4BS Tel: 020 7409 2992 Email: naseem@ri.ac.uk Website: http://www.ri.ac.uk/DFRL *** The RI is a Registered Charity (Number 227938) *** ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Fri Dec 7 09:13:19 2001 Received: from rbadb1.RBACPXCLU.BAS.ROCHE.COM ([196.3.50.190]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB7EDIi02461 for ; Fri, 7 Dec 2001 09:13:19 -0500 Received: from CONVERSION-DAEMON.Roche.COM by Roche.COM (PMDF V6.0-025 #47170) id <01KBLAGRA58097LMQJ@Roche.COM> for chemistry@ccl.net; Fri, 07 Dec 2001 15:11:20 +0100 Received: from rbamsemcn1.bas.roche.com (rbamsemcn1.bas.roche.com [145.245.211.139]) by Roche.COM (PMDF V6.0-025 #47170) with ESMTP id <01KBLAGIQA689AYX6D@Roche.COM>; Fri, 07 Dec 2001 15:11:07 +0100 Received: by rbamsemcn1.bas.roche.com with Internet Mail Service (5.5.2653.19) id ; Fri, 07 Dec 2001 15:11:44 +0100 Content-return: allowed Date: Fri, 07 Dec 2001 15:11:43 +0100 From: "Borosy, Andras {Basi~Basel}" Subject: RE: Package for neural network? To: "'Renxiao Wang'" , chemistry@ccl.net Message-id: <5FBD82D1CB46D511AAEA0002A55C6F5202AAAA06@rbamsem3.bas.roche.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id fB7EDJi02462 Dear Colleague, > I would like to apply neural network to my work to build a > QSAR model. I guess there are already some packages available > for doing this kind of job. Please recommend your favorite to > me and point out where to get it. I will put back the summary. Good idea. I used 3DNet for this purpose. I do not know if it available commercially (A.P. Borosy, P. Matyus, K. Keseru, Chemometrics & Int. Lab. Syst. 54, 107-122, 2000.) Theoretically any ANN with supervised learning is capable for that. See http://www.emsl.pnl.gov:2080/proj/neuron/neural/systems/software.html#131 Stuttgart Neural Network System is a very good choice, because it is a complex, powerfull application, run in many op. syst and free. http://www-ra.informatik.uni-tuebingen.de/SNNS/ Best wishes, András Borosy Basilea Pharmaceutica Ltd POB 3255, 65/316B 4002 Basel tel: +41-61-6885469 fax: +41-61-6882139 www.basileapharma.com From chemistry-request@server.ccl.net Fri Dec 7 09:44:33 2001 Received: from bute.st-andrews.ac.uk (im17@[138.251.12.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB7EiWi03583 for ; Fri, 7 Dec 2001 09:44:32 -0500 Received: from localhost (im17@localhost) by bute.st-andrews.ac.uk (8.9.1a/8.9.1) with SMTP id OAA04622; Fri, 7 Dec 2001 14:44:18 GMT Date: Fri, 7 Dec 2001 14:44:17 +0000 (GMT) From: Ibrahim Moustafa X-Sender: im17@st-andrews.ac.uk To: "nepenthes@vplaces.net" cc: "chemistry@ccl.net" Subject: Re: CCL:calculate/visualize electrostatic changes for protein-ligand In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Rowyna, I think all programs dealing with macromolecules have charge parameters for their atom types. When you load charges onto your protein the program just assaign charges to its atoms not more. After you dock the ligand the program still assign the same charge to the same atom type so you will not see different charges. Of course in the real system charges might be modified more or less but to account for that you need QM calculation which is not available so far for large molecules like proteins. I suggest you can calculate the electrostaic potential or the electric field for the free and the bound protein; you'll be able to see changes in ESP. Hope this can help. Ibrahim Name :Ibrahim M.Moustafa Mail address :Center for Biomolecular Science, BIOMOLECULAR SCIENCE BUILDING, North Haugh,St-Andrews, Fife,KY16 9ST Scotland,U.K. Tel :+44(0)1334-467257 E-mail :im17@st-andrews.ac.uk On Fri, 7 Dec 2001, nepenthes@vplaces.net wrote: > Dear CCLers, > > I'm trying to get a comparison of the changes in the electrostatic charges of a protein before and after docking a ligand It would be nice to get details of the changes and also a visual of the distribution of charges. I tried to use InsightII by merging the ligand and unbound protein together but the charges did not change at all (as seen by the output file of the charges etc). I'm quite sure there must be some changes when a ligand binds. I might be doing it wrong so I would be glad for any suggestions as to how I can perform this. I think Delphi can manage this but I would prefer to try with a free software if available. > > Thank you all for your time. > > Regards, > Rowyna K. > > > -------------------------------------------------------------------- > mail2web - Check your email from the web at > http://mail2web.com/ . > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Fri Dec 7 10:05:16 2001 Received: from oxygen.chem.nthu.edu.tw ([140.114.45.223]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB7F5Gi04320 for ; Fri, 7 Dec 2001 10:05:16 -0500 Received: by oxygen.chem.nthu.edu.tw (Postfix, from userid 212) id 72F0B154D0; Fri, 7 Dec 2001 23:05:02 +0800 (CST) Date: Fri, 7 Dec 2001 23:05:02 +0800 From: chem@oxygen.chem.nthu.edu.tw To: chemistry@ccl.net Subject: Re: CCL:Gaussian 98 benchmark for PC systems Message-ID: <20011207230502.A23543@OXYGEN.chem.nthu.edu.tw> References: <20011206011124.A19953@OXYGEN.chem.nthu.edu.tw> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i In-Reply-To: <20011206011124.A19953@OXYGEN.chem.nthu.edu.tw>; from chem@oxygen.chem.nthu.edu.tw on Thu, Dec 06, 2001 at 01:11:24AM +0800 Dear Listers, There are several persons asking about the makefile to compile Gaussian 98 with Intel Fortran compiler. We'll post the detail on our website after we make sure that it won't violate the licence agreement of Gaussian. Sincerely -- Yu, Jen-Shiang Kenny // jsyu@Platinum.chem.nthu.edu.tw http://oxygen.chem.nthu.edu.tw/~jsyu Theoretical Chemistry Lab, Department of Chemistry, National Tsing Hua University Hsinchu 300, TAIWAN