[gmx-users] dssp_index file

[Ahmet Yıldırım]

Sorry. Problem is solved. Helix4 includes 7 residues. I selected residues beside of atoms. Thanks.

Ahmet Yıldırım


25 Ağu 2014 tarihinde 21:34 saatinde, Justin Lemkul <jalemkul at vt.edu> şunları yazdı:

> 
> 
>> 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
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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
> 
> ==================================================
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> Gromacs Users mailing list
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