[gmx-users] DSSP with custom residues

[leila salimi]

Hi Justin,

I am also busy by DSSP analysis. I am interested to know what the
difference between do_dssp and dssp is?

Regards,
Leila

On Tue, Apr 26, 2016 at 3:00 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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