[gmx-users] dssp_index file

[Justin Lemkul]

On 8/25/14, 2:32 PM, Ahmet Yıldırım wrote:
> make_ndx -f topol.tpr -o helix4.ndx
> a 222 223 224 225 226 227 228
> q
>

So what are these atoms?

-Justin

> Structure has both chain A and chain B, includes 458 atoms except solvent.
>
> But dssp doesnt give any error when I created an index file including 201,211,...,228 atoms. This is strange?
>
> Ahmet Yıldırım
>
>
> 25 Ağu 2014 tarihinde 21:12 saatinde, Justin Lemkul <jalemkul at vt.edu> şunları yazdı:
>
>>
>>
>>> On 8/25/14, 2:09 PM, Ahmet Yıldırım wrote:
>>> I am using Gromacs 4.5.5 and old dssp (not dssp 2.x). Dssp is exist in usr/local/bin/dssp. It is executable.
>>>
>>> I dont have any error when I used the following command:
>>> do_dssp -f traj.xtc -s topol.tpr
>>> Select a group: 1 (protein)
>>>
>>> But I get the error when I used the index file with do_dssp. The index file includes a helix. I think dssp doesnt do the analysis of a helix/betasheet/coil...?
>>
>> If it fails when running your index group, that indicates the contents of the group are invalid or in some way problematic.  How did you create the group? What is in it?
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> 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 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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