From chemistry-request@server.ccl.net Wed May 8 01:52:54 2002 Received: from smtpout.mac.com ([204.179.120.86]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g485qsV19732 for ; Wed, 8 May 2002 01:52:54 -0400 Received: from smtp-relay03-en1.mac.com (smtp-relay03-en1 [10.13.10.222]) by smtpout.mac.com (8.12.1/8.10.2/1.0) with ESMTP id g485qNEM002761 for ; Tue, 7 May 2002 22:52:23 -0700 (PDT) Received: from asmtp01.mac.com (asmtp01-qfe3 [10.13.10.65]) by smtp-relay03-en1.mac.com (8.12.1/8.12.1/1.0) with ESMTP id g485qIC7027102 for ; Tue, 7 May 2002 22:52:18 -0700 (PDT) Received: from [10.10.130.81] ([142.165.217.186]) by asmtp01.mac.com (Netscape Messaging Server 4.15 asmtp01 Jun 21 2001 23:53:48) with ESMTP id GVS2Z600.92T for ; Tue, 7 May 2002 22:52:18 -0700 User-Agent: Microsoft-Entourage/10.0.0.1331 Date: Tue, 07 May 2002 23:52:10 -0500 Subject: GAMESS - Mac OS X??? From: "H. Martin Gillis" To: Message-ID: In-Reply-To: Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Hi, I just installed GAMESS for Mac OS X and ran into this warning when I tried to run any of the example files: --------------- The GAMESS executable gamess.00.x or else the DDIKICK executable ddikick.x could not be found in directory ./, or else they did not properly link to executable permission. --------------- Does anyone know how I can fix this??? -Thanks in advance, -Martin -- H. Martin Gillis 1105-101 Cumberland, Ave., S Saskatoon, SK S7N 1L5 CANADA (306) 652-7797 - Home (306) 966-4690 - Work -- From chemistry-request@server.ccl.net Wed May 8 06:16:30 2002 Received: from smtpscan-nl1.vscan.dsm-group.com ([163.175.162.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g48AGTV28152 for ; Wed, 8 May 2002 06:16:29 -0400 Received: from nlgln20ntms920.GLN20.DSM-GROUP.COM (localhost [127.0.0.1]) by smtpscan-nl1.vscan.dsm-group.com (8.9.3/8.8.5-1.2.2m-19990317) with ESMTP id MAA20210 for ; Wed, 8 May 2002 12:16:28 +0200 (MET DST) Received: by nlgln20ntms920.gln20.dsm-group.com with Internet Mail Service (5.5.2653.19) id <21S04196>; Wed, 8 May 2002 12:16:28 +0200 Message-ID: <6D47A7D05774D411959200508BDF739A0243828A@nlgln50ntms001.gln51.dsm-group.com> From: "Coussens, Betty" To: "'chemistry@ccl.net'" Subject: External parameters for Mopac calculations Date: Wed, 8 May 2002 12:16:09 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Dear all, I want to perform computations on Mg containing systems using Mopac6.0 and found an article in which a magnesium parameter set has been published for use with AM1 (i.e. J. Chem. Phys. B, vol. 102(41), 1998, 8083). I want to plug in these parameters into Mopac6.0 by using the keyword EXTERNAL=filename with filename the name of a file containing the new parameter set in the format Mg and terminated by a blank line. However, I appear to do something wrong as I keep getting the message 'SOME ELEMENTS HAVE BEEN SPECIFIED FOR WHICH NO PARAMETERS ARE AVAILABLE. CALCULATION STOPPED'. Has anybody an idea about what could possibly be wrong? Thanks in advance for the help! Betty Disclaimer 1. This e-mail is for the intended recipient only. If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. 2. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately. This e-mail is confidential and may be legally privileged. DSM does not guarantee that the information sent and/or received by or with this e-mail is correct and does not accept any liability for damages related thereto. From chemistry-request@server.ccl.net Wed May 8 10:01:51 2002 Received: from rwcrmhc52.attbi.com ([216.148.227.88]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g48E1pV00861 for ; Wed, 8 May 2002 10:01:51 -0400 Received: from C1353359A ([12.228.119.53]) by rwcrmhc52.attbi.com (InterMail vM.4.01.03.27 201-229-121-127-20010626) with SMTP id <20020508140145.MQOJ25294.rwcrmhc52.attbi.com@C1353359A>; Wed, 8 May 2002 14:01:45 +0000 Reply-To: From: "Mark Thompson" To: "Coussens, Betty" , Subject: RE: External parameters for Mopac calculations Date: Wed, 8 May 2002 07:06:25 -0700 Message-ID: <000a01c1f699$8a178170$0300a8c0@attbi.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 Importance: Normal In-Reply-To: <6D47A7D05774D411959200508BDF739A0243828A@nlgln50ntms001.gln51.dsm-group.com> Dear Betty, Its far easier to add new parameters to ArgusLab to run your PM3/AM1 calculations. All parameters are stored in formatted text files for MNDO, AM1, PM3, EHT, and ZINDO. This approach has been particularly popular with ZINDO users who want to calculate spectra with new or modified atomic parameters. You can get ArgusLab at http://www.arguslab.com Cheers, Mark ================================= Mark Thompson, Ph.D. Planaria Software Seattle, WA. http://www.arguslab.com ================================= > -----Original Message----- > From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On > Behalf Of Coussens, Betty > Sent: Wednesday, May 08, 2002 3:16 AM > To: 'chemistry@ccl.net' > Subject: CCL:External parameters for Mopac calculations > > > Dear all, > > I want to perform computations on Mg containing systems using Mopac6.0 and > found an article in which a magnesium parameter set has been published for > use with AM1 (i.e. J. Chem. Phys. B, vol. 102(41), 1998, 8083). I want to > plug in these parameters into Mopac6.0 by using the keyword > EXTERNAL=filename with filename the name of a file containing the new > parameter set in the format Mg and > terminated by a blank line. However, I appear to do something wrong as I > keep getting the message 'SOME ELEMENTS HAVE BEEN SPECIFIED FOR WHICH NO > PARAMETERS ARE AVAILABLE. CALCULATION STOPPED'. Has anybody an > idea about > what could possibly be wrong? > > Thanks in advance for the help! > > Betty > From chemistry-request@server.ccl.net Wed May 8 13:25:48 2002 Received: from relay-1m.club-internet.fr ([194.158.104.40]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g48HPlV07378 for ; Wed, 8 May 2002 13:25:48 -0400 Received: from sungam (vlm2a1-187.n.club-internet.fr [212.195.24.187]) by relay-1m.club-internet.fr (Postfix) with SMTP id 8810D16F1 for ; Wed, 8 May 2002 19:25:45 +0200 (CEST) Message-ID: <001101c1f6b5$934a0620$bb18c3d4@sungam> From: "Julien MICHEL" To: References: <6D47A7D05774D411959200508BDF739A0243828A@nlgln50ntms001.gln51.dsm-group.com> Subject: Computing energies of binding Date: Wed, 8 May 2002 19:22:58 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6600 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 Dear CCLers, I am currently trying to evaluate energies of interaction between a group of peptides and it's receptor. I am particularly interested in computing these energies with solvated compounds. I was thinking to build a thermodynamic cycle. The in vacuo step seems clear enough to me, but I was wondering how I should consider the problem of solvation. It seems to me that my calculations would be inconsistent if I'm not careful. Assuming I need N molecules of water to solvate my ligand and M molecules to solvate my Receptor. Upon, solvating my in vacuo complex, should I use N+M molecules of water so that my system size is consistent ? I can see another way to consider the cycle. I could start with a big box filled with water, add either ligand, receptor or complex depending on the calculation desired and eliminate overlapping water molecules. But then the size wouldn't be consistent anymore. I am also wondering how one can define a system as properly solvated. I would like to keep computational expenses low and ideally I'd like to use a layer of a few angstroms on each compounds and restrain the solvent molecules from moving away from the system using a small distance dependant restrain (from the centre of mass). Best regards, Julien MICHEL From chemistry-request@server.ccl.net Wed May 8 16:33:43 2002 Received: from freyr.chem.washington.edu ([128.95.128.138]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g48KXhV11053 for ; Wed, 8 May 2002 16:33:43 -0400 Received: from localhost (fer@localhost) by freyr.chem.washington.edu (8.11.6/8.11.6) with ESMTP id g48KWaj16412; Wed, 8 May 2002 13:32:36 -0700 Date: Wed, 8 May 2002 13:32:36 -0700 (PDT) From: "Fernando D. Vila" To: Computational Chemistry List cc: Subject: Finite Field PT in Gaussian Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi.. I don't send questions to the CCL very often, but it looks like this week I'm going to send a couple.. And this one is looong.. :-) I have been trying to calculate the dipole-quadrupole (A) and quadrupole-quadrupole (C) polarizabilities of water by means of Finite Field Perturbation Theory (FFPT) using Gaussian 98 Rev A.7. I have previous experience with this method, I've used it to calculate dipole moments and dipole polarizabilities. Now I've run into some trouble because I need to transform the Cartesian-based properties that Gaussian generates into the traceless ones. Right now I'm pretty confused, so I'll try to explain the problem as clearly as I can. I think the main question is: what is the expression of the perturbation Hamiltonian used by Gaussian?? I have found that when a dipole perturbation is applied (lets say, in the z direction), the perturbed energy can be written as: E = E0 + Mz * Vz where E0 is the unperturbed energy, Mz is the Cartesian z component of the dipole moment and Vz is the magnitude of the perturbation. I have checked and the Mz moment is identical to the one reported at the end by Gaussian. This is reasonable, the problem comes when you check that for a quadrupole perturbation the SAME formula is valid. Now, if the standard Cartesian perturbation Hamiltonian was used, the formula should be E = E0 + 1/2 * Mzz * Vzz I did the same for the octupole and the hexadecapole and the apparent Hamiltonian used by Gaussian is H' = Mi * Vi + Mij * Vij + Mijk * Vijk + Mijkl * Vijkl where the repeated indices are summed. This series is missing the 1/n! coefficients in front of each term. I tried checking if these coefficients are folded into the Cartesian moments, but this is not the case: when the Cartesian moments are used to calculate the traceless moments, the results are exactly correct, so no coefficients are included (the moments are simple the Cartesian components). Since I don't know what perturbation is being used, I can't derive the transformation relation that would take the Cartesian components of, say, the dipole-quadrupole polarizability and give me the ones associated with the traceless operators. What is really frustrating is that the Gaussian manual is extremely terse in the explanation of what is being done. Moreover, I've found that the warning in the manual regarding the sign ("be careful of the choice of sign convention when interpreting the results") is quite misleading: according to usual standards, what Gaussian is using are not electric fields but potential gradients. Let me say, finally, that I have actually gone into the code to see if there were any more explanatory comments, without success.. Hope anybody can help, thanks in advance.. Fer. ******************************************************************************* Fernando D. Vila Voice (206)616-3207 Department of Chemistry Fax (206)685-8665 University of Washington E-mail fdv@u.washington.edu Seattle, WA 98195, USA WWW http://faculty.washington.edu/fdv ******************************************************************************* From chemistry-request@server.ccl.net Wed May 8 11:42:05 2002 Received: from postfix2.uni-muenster.de ([128.176.188.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g48Fg4V02896 for ; Wed, 8 May 2002 11:42:04 -0400 Received: from ZIVUNIX.UNI-MUENSTER.DE (ZIVUNIX.UNI-MUENSTER.DE [128.176.4.4]) by postfix2.uni-muenster.de (Postfix) with ESMTP id DB78F1005; Wed, 8 May 2002 17:41:59 +0200 (MES) Date: Wed, 8 May 2002 17:41:59 +0200 (MES) From: Ernst-Ulrich Wuerthwein To: "Coussens, Betty" Cc: "'chemistry@ccl.net'" Subject: Re: CCL:External parameters for Mopac calculations In-Reply-To: <6D47A7D05774D411959200508BDF739A0243828A@nlgln50ntms001.gln51.dsm-group.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The correct reference for the AM1-Mg parameters is as follows: M. C. Hutter, J. R. Reimers, N. S. Hush, J. Phys. Chem. B 1998, 102, 8080-8090 E.-U. Wuerthwein On Wed, 8 May 2002, Coussens, Betty wrote: > Date: Wed, 8 May 2002 12:16:09 +0200 > From: "Coussens, Betty" > To: "'chemistry@ccl.net'" > Subject: CCL:External parameters for Mopac calculations > > Dear all, > > I want to perform computations on Mg containing systems using Mopac6.0 and > found an article in which a magnesium parameter set has been published for > use with AM1 (i.e. J. Chem. Phys. B, vol. 102(41), 1998, 8083). I want to > plug in these parameters into Mopac6.0 by using the keyword > EXTERNAL=filename with filename the name of a file containing the new > parameter set in the format Mg and > terminated by a blank line. However, I appear to do something wrong as I > keep getting the message 'SOME ELEMENTS HAVE BEEN SPECIFIED FOR WHICH NO > PARAMETERS ARE AVAILABLE. CALCULATION STOPPED'. Has anybody an idea about > what could possibly be wrong? > > Thanks in advance for the help! > > Betty > > Disclaimer > 1. This e-mail is for the intended recipient only. If you have received it > by mistake please let us know by reply and then delete it from your system; > access, disclosure, copying, distribution or reliance on any of it by anyone > else is prohibited. > > 2. If you as intended recipient have received this e-mail incorrectly, > please notify the sender (via e-mail) immediately. This e-mail is > confidential and may be legally privileged. DSM does not guarantee that the > information sent and/or received by or with this e-mail is correct and does > not accept any liability for damages related thereto. > > > -= 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 > > >