[gmx-users] DSSP with custom residues
jalemkul at vt.edu
Tue Apr 26 15:00:31 CEST 2016
On 4/26/16 8:57 AM, Stephanie Jephthah wrote:
> I'm simulating a protein conjugate and thus uses custom residues. Is there
> any way to make the dssp program aware of the custom residues (and does it
> make sense to do so)? I'm using gromacs 4.6.7 and the "new" dssp. I'm
> assuming that the problem is not with do_dssp but with dssp, but please
> correct me if I'm wrong.
If you've got custom residues as integral parts of the protein, they need to be
defined as such in residuetypes.dat, or otherwise defined in a suitable custom
index group. Presumably you have to have done one or the other before running
the simulation. If the custom residues have normal amino acid backbone
features, doing DSSP analysis makes sense. If something is failing, run dssp
directly, not via do_dssp, to determine if the failure is within dssp or do_dssp.
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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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