[gmx-users] dssp_index file

[Ahmet Yıldırım]

make_ndx -f topol.tpr -o helix4.ndx
a 222 223 224 225 226 227 228
q

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
> 
> -- 
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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