[gmx-users] do_dssp

Justin A. Lemkul jalemkul at vt.edu
Fri Aug 15 13:47:04 CEST 2008

minnale wrote:
> Hi all,
>   I want to analyse secondary struture of my protein which have run MD 
> for 7ns. I have checked in archives about do_dssp, found that can use 
> only .pdb file instead of .trr and .tpr. Then if type command with -h it 
> has it has given .xtc, .tpr,  and .ndx should use.

Where does it say that you can't use your trajectory?  That's certainly 
incorrect.  The standalone dssp program (which you must obtain separately from 
the DSSP site) can only run on a single .pdb file, but Gromacs makes use of the 
dssp executable such that it can be used with trajectories.

Hence the lovely plots you see in the literature.


> I am bit confusing with about do_dssp command.
> Can you explain me clearly. 
> Thanks in advance.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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