[gmx-users] DSSP with custom residues

[Justin Lemkul]

On 4/26/16 8:57 AM, Stephanie Jephthah wrote:
> Hi!
>
> 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

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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