[gmx-users] dssp_index file

[Ahmet Yıldırım]

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...?

Ahmet Yıldırım


25 Ağu 2014 tarihinde 19:46 saatinde, Justin Lemkul <jalemkul at vt.edu> şunları yazdı:

> 
> 
>> On 8/25/14, 10:08 AM, Ahmet yıldırım wrote:
>> Dear users,
>> 
>> I want to analysis the change of a helix in secondary structure during
>> simulation time but I get the following error. Why am I getting this error?
>> 
>> do_dssp -f traj.xtc -s topol.tpr -o ss-helix4.xpm -sc ss-helix4.xvg -n
>> helix4.ndx
>> Select a group: 19 (helix4 includes 7 atom)
>> 
>> Fatal error:
>> Failed to execute command: /usr/local/bin/dssp -na ddUYNXx9 dd1AmuF4 >
>> /dev/null 2> /dev/null
> 
> /usr/local/bin/dssp either doesn't exist, is the wrong version (use do_dssp -ver) or is not executable.
> 
> -Justin
> 
> -- 
> ==================================================
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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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