[gmx-users] dssp_index file
ahmedo047 at gmail.com
Mon Aug 25 20:32:54 CEST 2014
make_ndx -f topol.tpr -o helix4.ndx
a 222 223 224 225 226 227 228
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?
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 A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
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