[gmx-users] DSSP with custom residues

[Justin Lemkul]

On 4/26/16 9:10 AM, leila salimi wrote:
> Hi Justin,
>
> I am also busy by DSSP analysis. I am interested to know what the
> difference between do_dssp and dssp is?
>

dssp is a binary that actually carries out the DSSP analysis; it is not a 
GROMACS program but is downloaded from an external source.  do_dssp is a GROMACS 
module that is just a wrapper - it runs through a trajectory, pulls out the 
coordinates to a temporary file (those ddXXXX files that show up), passes those 
coordinates to dssp, and records the output.  GROMACS doesn't do secondary 
structure calculations natively, instead relying on dssp.

-Justin

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

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

==================================================