Hi Justin, are you guys planning anything to make pdb2gmx understand the CHARMM patch residues? We have some python scripts which generate new residues based on the patch residues, which allows us to simulate branched molecules (e.g. glycosylation or lignin). But that approach is very suboptimal and I think a more general approach would be very nice.
Roland On Tue, Oct 8, 2013 at 4:16 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > All, > > I am pleased to announce the immediate availability of the latest CHARMM36 > force > field in GROMACS format. You can obtain the archive from our lab's > website at > http://mackerell.umaryland.edu/CHARMM_ff_params.html. > > The present version contains up-to-date parameters for proteins, nucleic > acids, > lipids, some carbohydrates, CGenFF version 2b7, and a variety of of other > small > molecules. Please refer to forcefield.doc, which contains a list of > citations > that describe the parameters, as well as the CHARMM force field files that > were > used to generate the distribution. > > We have validated the parameters by comparing energies of a wide variety of > molecules within CHARMM and GROMACS and have found excellent agreement > between > the two. If anyone has any issues or questions, please feel free to post > them > to this list or directly to me at the email address below. > > Happy simulating! > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
