Hi Oliver, Apologies for the late reply. The comparison you have showed us has been done for a DNA fragment. Do you believe that negligible errors can also be obtained for proteins using the amber99sb force field?
thanks, Thomas On 22 November 2011 11:58, Oliver Grant <[email protected]> wrote: > Hi there, > > Acpype does the conversion for you and the results from their own testing > are here: > http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx > > For reproducing experimental data I would look in the original force-field > publications. > > Oliver > > > On Mon, Nov 21, 2011 at 8:21 PM, Michael Shirts <[email protected]>wrote: > >> > Is anyone aware of any benchmark analysis about the implementation of >> the >> > amber99sb force field (or any of its variants: 99sb-ildn, 99sb-nmr) in >> > GROMACS and AMBER. I am interested to know in what extend the energies >> > correlate and if the results agree with experimental data. >> >> Whether the results compare agree with experimental data is irrelevant >> to the correctness of the implementation -- that has to do with the >> validity of AMBER99sb to begin with. The only question is, do GROMACS >> and AMBER give the same energies for the same configurations? >> >> I actually do not know the answer, and would be interested to hear if >> it's been tested. http://ffamber.cnsm.csulb.edu/ does not appear to >> have the very comprehensive tests that appear for earlier models at >> the current time. I SUSPECT there should not be a problem, since >> AMBER99sb just changed a couple of torsions, so errors are unlikely >> (though in theory possible). >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >> > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: [email protected] [email protected] website: https://sites.google.com/site/thomasevangelidishomepage/
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