From chemistry-request@server.ccl.net Mon Sep 4 23:21:45 2000 Received: from cougar.it.wsu.edu (root@cougar.it.wsu.edu [134.121.1.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA00471 for ; Mon, 4 Sep 2000 23:21:45 -0400 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by cougar.it.wsu.edu (8.9.3/8.9.3) with SMTP id UAA31545 for ; Mon, 4 Sep 2000 20:21:39 -0700 (PDT) Message-ID: <002601c016e8$67acb750$b4297986@chem.wsu.edu> From: "Phillip Matz" To: "CCL" Subject: Fw: g98 compilation in Suse 6.4 Date: Mon, 4 Sep 2000 20:21:39 -0700 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 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Dear Philip, Thanks for your response. I believe your solution is the one I am looking for. However, my portland compiler is close to expiry and it's very slow now. Furthermore, I have got a binary version of g98 and therefore I would leave it to you to post your suggestion to CCL in case someone might have a follow-up enquiry. Again, many thanks for your suggestion which is certainly helpful to me any my colleagues. Best Regards, Jerry ****************************************************************** * Jerry Chun Chung CHAN chan@uni-muenster.de * * Universitaet Muenster * * Institut fuer Physikalische Chemie fax: 0049-251-83-29159 * * Schlossplatz 4-7 voice: 0049-251-83-29157 * * D-48149 Muenster * * Germany * ****************************************************************** ----- Original Message ----- From: Phillip Matz To: chan@uni-muenster.de Sent: Saturday, September 02, 2000 7:55 PM Subject: g98 compilation in Suse 6.4 Hello! Regarding your message posted on the CCL concerning g98 compiling. I believe your problem lies not with your linux distribution (SUSE 6.4), rather the compiler error is due to your processor (K6) and the default processor listed in the g98 i386.make file for the Portland Group compiler. In the g98 i386.make file you will notice the default processor type is "-tp p6", another processor type selection is available but commented out, i.e. "-tp p5". For the AMD K6, the Portland Group compiler needs to think it is compiling for a Pentium processor, so comment out the "-tp p6" line and uncomment the "-tp p5" line and recompile. This should do the trick (it did for me). A side note, the above solution for the K6 is not needed for the ATHLON. The Portland Group compiler will work with the "-tp p6" switch and an ATHLON. In fact, for G98 the compiled code will run 5~10% slower if you do use the "-tp p5" switch (I have done this and I do have the hard numbers to back up my statements). I am not posting this to CCL as I am not a member yet, I subscribed earlier today but I have not received my confirmation yet. Feel free to repost this message on CCL as it will surely help others. I will repost it on CCL as soon as I can but that may take a while. Good Luck! Phillip Matz matz@wsunix.wsu.edu From chemistry-request@server.ccl.net Tue Sep 5 08:09:00 2000 Received: from uscmail.usc.es (uscmail.usc.es [193.144.75.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA03451 for ; Tue, 5 Sep 2000 08:08:59 -0400 Received: from qogolem (qogolem.usc.es [193.144.74.235]) by uscmail.usc.es (8.9.1/8.9.1) with SMTP id OAA21718 for ; Tue, 5 Sep 2000 14:08:11 +0200 (MET DST) Message-ID: <001301c01731$a56dd990$eb4a90c1@qogolem.usc.es> From: "Armando Navarro" To: Subject: nonvdw gamess keyword Date: Tue, 5 Sep 2000 14:05:27 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000E_01C01742.57C0AFE0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 This is a multi-part message in MIME format. ------=_NextPart_000_000E_01C01742.57C0AFE0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Members: Does anybody know what the correct syntax for gamessUS nonvdw keyword = is? For instance if I want to bond atoms pairs 3,4 and 7,8 how must I write = my input? Armando Navarro Departamento de quimica Organica. Facultade de quimica Universidade de Santiago de Compostela=20 Spain e-mail: qoajnv@usc.es ------=_NextPart_000_000E_01C01742.57C0AFE0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Members:
Does anybody know what the correct = syntax for=20 gamessUS nonvdw keyword is?
For instance if I want to bond atoms = pairs 3,4=20 and 7,8 how must I write my input?
Armando Navarro
Departamento de quimica Organica. = Facultade de=20 quimica
Universidade de Santiago de = Compostela=20
Spain
e-mail: qoajnv@usc.es
 
------=_NextPart_000_000E_01C01742.57C0AFE0-- From chemistry-request@server.ccl.net Tue Sep 5 16:05:42 2000 Received: from gandalf.cber.nih.gov (gandalf.cber.nih.gov [128.231.52.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA05332 for ; Tue, 5 Sep 2000 16:05:41 -0400 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id QAA65119; Tue, 5 Sep 2000 16:08:48 -0400 (EDT) Date: Tue, 5 Sep 2000 16:08:48 -0400 From: Rick Venable To: Don Gregory cc: CHEMISTRY@ccl.net Subject: Re: CCL:I/O in Charmm In-Reply-To: <4.3.1.2.20000903162527.00b32d20@146.202.6.130> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I'd like to add a couple additional comments, from the perspective of an experienced user of the academic version of CHARMM (as opposed to MSI's CHARMm). My recommendation to the original poster was to create the phosphorylated ribose topology (RESIdue) by hand editing a copy of a nucleic acid topology file, paying careful attention to atom parameter types. This is probably the most reliable way, assuming all the needed parameters are available (they should be, for phospho-ribose). On Sun, 3 Sep 2000, Don Gregory wrote: > Really, there are two separate issues here; (a) using InsightII to create > CHARMm input files, and (b) what to do when a chosen force-field > is missing parameters. Since the original question referred to one of the academic topology files, a potential third issue is using mixed parameters; in general, it's a bad idea. RTF/PARAM files are developed and must be used with explicit pairings, and there are several sets of these files available today from various development efforts, both academic and commercial. Further, one should not "borrow" parameters and RTF files from one development effort for use with another, at least not without detailed testing. One fundamental difference for the academic parameters is that they assume less transferrability than e.g. the commercial sets available from MSI with Quanta and InSightII. > The easy one first: Indeed, InsightII can write CHARMm PSF and > RTF files. Whenever your research leads you to modify > the (more or less) 'standard' molecule/residue types that > are provided in the RTF files that come with InsightII, we > heartily recommend you use the PSF creation capabilities > of InsightII to make the 'whole-system' unique molecular > topology description that CHARMm needs, i.e. the PSF file. > That is what this capability is intended for. As noted in Don Gregory's reply, this assumes the use of the CFF parameters, one of the several development efforts. As I note above, one shouldn't try to combine a CFF-derived molecular description (RTF, PSF) with e.g. the academic parameters w/o testing. I agree whole-heartedly with Don Gregory that any such extension to an existing or default topology and parameter set should be documented in any publications using the changes, along with how the changes were tested. Some journals even insist that you do so. In general, caution and attention to detail are needed when adding new molecules to CHARMM, especially when using the academic parameters. Even more work is needed if it turns out that there are missing parameters. Although it may be possible to point-and-click your way to a molecular description and parameters w/o any gross flaws, I recommend a detailed comparison to existing similar residues before going too far with any detailed molecular mechanics studies. A final note-- my personal experiences with programs such as ChemNote (supplied w. Quanta) for building new CHARMM residues has generally been unsatisfactory. I haven't tried the InSightII tool (we don't use CFF). Original question: > At 06:37 PM 9/3/00 -0400, Xiang(Simon) Wang wrote: > >Can someone help me on how to read small molecule structure in Charmm? > >For example, phosphoribosyldiphosphate (PRPP), which can not be found in > >top_all22_model.inp file. I could get the PSF file from InsightII. But > >when running, Charmm gave the warning of lacking of parameters. Can > >someone help me out of it? -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or Rick_Venable@nih.gov | \ / |=| position of the FDA; for that, rvenable@speakeasy.org \/ |=| see http://www.fda.gov )