What you mean is that I can use the AMBER parameters on the website (http://sites.pharmacy.manchester.ac.uk/bryce/amber <http://sites.pharmacy.manchester.ac.uk/bryce/amber>) and need to convert the format of the parameters to the one that GROMACS is compatible with in the .rtp entries? > 在 2016年6月3日，上午5:50，Justin Lemkul <[email protected]> 写道： > > > > On 6/2/16 10:55 AM, YanhuaOuyang wrote: >> Dear Gromacs users, >> >> I am going to run a MD of a 20-residue protein which is phosphorylated on the >> Serine and Threonine residues with AMBER ff99SB-ILDN force field using >> Gromacs5.0. When I run gmx pdb2gmx and choose AMBER ff99SB-ILDN force field, >> it appears: fatal error: residues SEP not found in residue topology >> database. >> >> I search some papers, and they say that we need to add add force fields >> parameters for the phosphorylated amino acids to the force filed parameter >> files. But I do not know how to add force fields parameters for the >> phosphorylated amino acids. Could anyone knows how to construct a model for >> the phosphorylated protein? >> > > AMBER parameters are already available: > > http://sites.pharmacy.manchester.ac.uk/bryce/amber > > You just need to convert the format and build suitable .rtp entries. Or find > a force field that already has this done for you (CHARMM36, Gromos96 43a1p, > etc). > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > [email protected] | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to [email protected].
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