Re: [gmx-users] compatibility of MOPAC charges with GROMACS ?
On Wed, May 16, 2007 at 05:16:49PM -0700, David Mobley wrote: So what you really need to do, once you have worked out which forcfield you are going to use, go back to the documentation / papers for that particular forcefield, see how they generated the parameters, then use that same procedure for the new parameters / molecules you want to generated. Strangely enough, I recall writing almost exactly the same thing in response to a different user yesterday or the day before. It will sure be nice when the Wiki is working, then we only have to answer this once. ..and RTFW will replace RTFM.. marc ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] compatibility of MOPAC charges with GROMACS ?
Dear all I'm trying to assemble a topology entry for S-nitrosocysteine. Searching through the examples in the PDB revealed quite a spread of bond lengths and angles - the N=O bond ranges from 1.2 to 1.47A, for example. To get more rigorously derived figures, and to calculate charges, I thought of using MOPAC http://www.openmopac.net/index.html I imagine that the bond lengths and angles from MOPAC will be reliable. My question is really how compatible the charges are with the GROMACS topologies? Would you have any qualms about mixing and matching? Surely MOPAC's estimates must be better than human guesstimates or, despite its general wonderful usefulness, PRODRG's estimates? Are there other programs for this? Any thoughts welcome Regards Daniel -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] compatibility of MOPAC charges with GROMACS ?
To get more rigorously derived figures, and to calculate charges, I thought of using MOPAC http://www.openmopac.net/index.html I imagine that the bond lengths and angles from MOPAC will be reliable. My question is really how compatible the charges are with the GROMACS topologies? Would you have any qualms about mixing and matching? Surely MOPAC's estimates must be better than human guesstimates or, despite its general wonderful usefulness, PRODRG's estimates? Are there other programs for this? What it comes back to is how the forcefield you are using is constructed. It will have been done using a particular procedure for generating the partial charges, L-J interactions, bonding etc to fit some particular parameters. If you use a different procedure to generate yours and try to mix it with the forcefield, then there is an extremely good chance you will get out garbage. So what you really need to do, once you have worked out which forcfield you are going to use, go back to the documentation / papers for that particular forcefield, see how they generated the parameters, then use that same procedure for the new parameters / molecules you want to generated. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] compatibility of MOPAC charges with GROMACS ?
So what you really need to do, once you have worked out which forcfield you are going to use, go back to the documentation / papers for that particular forcefield, see how they generated the parameters, then use that same procedure for the new parameters / molecules you want to generated. Strangely enough, I recall writing almost exactly the same thing in response to a different user yesterday or the day before. It will sure be nice when the Wiki is working, then we only have to answer this once. David ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
