[gmx-users] do_dssp

[Justin A. Lemkul]

As a final note, it is probably better to use the .xtc file for analysis.  The 
do_dssp program is very slow, and I can only imagine that reading the 
full-precision trajectory will slow to an absolute crawl.

-Justin

Justin A. Lemkul wrote:
> 
> 
> 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.
> 
> -Justin
> 
>> 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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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