From chemistry-request@server.ccl.net Tue Oct 24 09:31:11 2000 Received: from web3407.mail.yahoo.com (web3401.mail.yahoo.com [204.71.203.55]) by server.ccl.net (8.8.7/8.8.7) with SMTP id JAA04171 for ; Tue, 24 Oct 2000 09:31:10 -0400 Message-ID: <20001024132859.11742.qmail@web3407.mail.yahoo.com> Received: from [136.142.109.175] by web3401.mail.yahoo.com; Tue, 24 Oct 2000 06:28:59 PDT Date: Tue, 24 Oct 2000 06:28:59 -0700 (PDT) From: Mary Boyden Subject: Summary: program to calc. internal coordinates and PED To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCL: Sincere thanks to all who replied to my question! Below I have printed my original email and a summary of the responses: >Dear CCL: > >I would like to find a program which will accept the >normal mode Cartesian coordinates from a Gaussian 98 >output file, convert them to internal coordinates, and >find the potential energy distribution for one of the >normal modes. Are there any (preferably free) >programs available that will accomplish this? > >I am a beginner and really appreciate all help. > >Thanks! >Mary Boyden > >Department of Chemistry >Unversity of Pittsburgh Responses: 1. "Try redong from A. Allouche: Allouche, Pourcin, Spectrochim Acta 1993,49A, 571. I am sure he is willing to make his program accessible to you. But you have to do the internal coordinate definition by yourself. Since for large molecules or clusters, there are often different 'complete' sets of internal coordinates (in the sense that they cover all vibrational degrees of freedom), it makes sense to leave the choice to the user..." 2. "You can look at the "Redong" program available >from QCPE. With slight modifications you can read the G98 output." The URL for the QPCE is: http://qcpe.chem.indiana.edu/ Also I wrote the following email to Gaussian: >I am doing frequency calculations using MP2 and have >been sucessful in obtaining the atomic displacements >in Cartesian coordinates. > > However, I would like to obtain the eigenvector of >the Hessian for one of the positive frequencies in >terms of internal coordinates. How can I obtain this >information...? Here is the response: "There is no facility in Gaussian for doing this transformation. While there is treatment of force constants over the subset of internal coordinates suitable for optimization it is not available for frequencies. This analysis can be done by some external programs, mostly from the spectroscopy community. We have one which we are working to make more generally available with a decent interface to G98 but I don't see it available for a few months." __________________________________________________ Do You Yahoo!? Yahoo! Messenger - Talk while you surf! It's FREE. http://im.yahoo.com/ From chemistry-request@server.ccl.net Tue Oct 24 09:33:57 2000 Received: from web3407.mail.yahoo.com (web3401.mail.yahoo.com [204.71.203.55]) by server.ccl.net (8.8.7/8.8.7) with SMTP id JAA04180 for ; Tue, 24 Oct 2000 09:33:56 -0400 Message-ID: <20001024133145.12051.qmail@web3407.mail.yahoo.com> Received: from [136.142.109.175] by web3401.mail.yahoo.com; Tue, 24 Oct 2000 06:31:45 PDT Date: Tue, 24 Oct 2000 06:31:45 -0700 (PDT) From: Mary Boyden Subject: Summary: program to calc. internal coordinates and PED To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCL: Sincere thanks to all who replied to my question! Below I have printed my original email and a summary of the responses: >Dear CCL: > >I would like to find a program which will accept the >normal mode Cartesian coordinates from a Gaussian 98 >output file, convert them to internal coordinates, and >find the potential energy distribution for one of the >normal modes. Are there any (preferably free) >programs available that will accomplish this? > >I am a beginner and really appreciate all help. > >Thanks! >Mary Boyden > >Department of Chemistry >Unversity of Pittsburgh Responses: 1. "Try redong from A. Allouche: Allouche, Pourcin, Spectrochim Acta 1993,49A, 571. I am sure he is willing to make his program accessible to you. But you have to do the internal coordinate definition by yourself. Since for large molecules or clusters, there are often different 'complete' sets of internal coordinates (in the sense that they cover all vibrational degrees of freedom), it makes sense to leave the choice to the user..." 2. "You can look at the "Redong" program available >from QCPE. With slight modifications you can read the G98 output." The URL for the QPCE is: http://qcpe.chem.indiana.edu/ Also, I wrote the following email to Gaussian: >I am doing frequency calculations using MP2 and have >been sucessful in obtaining the atomic displacements >in Cartesian coordinates. > > However, I would like to obtain the eigenvector of >the Hessian for one of the positive frequencies in >terms of internal coordinates. How can I obtain this >information...? Here is the response: "There is no facility in Gaussian for doing this transformation. While there is treatment of force constants over the subset of internal coordinates suitable for optimization it is not available for frequencies. This analysis can be done by some external programs, mostly from the spectroscopy community. We have one which we are working to make more generally available with a decent interface to G98 but I don't see it available for a few months." __________________________________________________ Do You Yahoo!? Yahoo! Messenger - Talk while you surf! It's FREE. http://im.yahoo.com/ From chemistry-request@server.ccl.net Tue Oct 24 15:49:37 2000 Received: from ouchem.chem.oakland.edu (ouchem.chem.oakland.edu [141.210.108.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA06163 for ; Tue, 24 Oct 2000 15:49:36 -0400 Received: from ouchem.chem.oakland.edu ([141.210.178.47]) by ouchem.chem.oakland.edu (8.11.0/8.11.0) with ESMTP id e9OJnXM04072 for ; Tue, 24 Oct 2000 15:49:33 -0400 (EDT) Message-ID: <39F61188.7F01DD54@ouchem.chem.oakland.edu> Date: Tue, 24 Oct 2000 15:47:37 -0700 From: Pedro Salvador X-Mailer: Mozilla 4.73C-CCK-MCD {C-UDP; EBM-APPLE} (Macintosh; U; PPC) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: g98 compiling error on Dec alpha Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Dear CCLers I'm trying to install g98 on a Compaq Tru64 UNIX V5.0A (Rev. 1094) machine with the Compaq C V6.1-019 and the Compaq Fortran V5.3-915 c and f77 compilers, respectively At the very beining of the installation i got this error on the cpp.c file cc: Error: bsd/cpp.c, line 1542: In this statement, "MAXINCLUDE" is not declared . (undeclared) if (incend >= &incdir[MAXINCLUDE]) ------------------------------------------^ *** Exit 1 Stop. Does anybody have experience on this platform? Any help will be appreciated thank you very much in advance From chemistry-request@server.ccl.net Tue Oct 24 15:56:30 2000 Received: from facepe.dqf.ufpe.br (root@facepe.dqf.ufpe.br [150.161.5.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA06224 for ; Tue, 24 Oct 2000 15:56:10 -0400 Received: from npd.ufpe.br (pipa.dqf.ufpe.br [150.161.5.24]) by facepe.dqf.ufpe.br (8.9.3/8.8.7) with ESMTP id RAA06465 for ; Tue, 24 Oct 2000 17:58:06 -0200 Message-ID: <39F5DADF.48979D4E@npd.ufpe.br> Date: Tue, 24 Oct 2000 16:54:23 -0200 From: Gerd Bruno Rocha X-Mailer: Mozilla 4.72 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Databases Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all, I am looking for any references (url, books, papers, etc.) on free access or publicly available databases which contain experimental data about dipole moment, ionization potentials, thermodynamic properties and crystallographic structures of organic molecules. Thanks in advance, ---- Gerd Bruno Rocha DQF - UFPE www.dqf.ufpe.br From chemistry-request@server.ccl.net Tue Oct 24 16:52:48 2000 Received: from postoffice.mail.cornell.edu (postoffice.mail.cornell.edu [132.236.56.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA06638 for ; Tue, 24 Oct 2000 16:52:48 -0400 Received: from cornell.edu (carbo2.foodsci.cornell.edu [132.236.147.61]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id QAA19318 for ; Tue, 24 Oct 2000 16:52:46 -0400 (EDT) Sender: dwood@cornell.edu Message-ID: <39F5F524.57E654F5@cornell.edu> Date: Tue, 24 Oct 2000 16:46:28 -0400 From: "Dr. Richard Wood" Organization: Cornell University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: A Charmm question Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all Is there a better way to constrain bonds containing hydrogens when heating other than using the command SHAKE? Richard Wood