[gmx-users] do_dssp

minnale minnale_gnos at rediffmail.com
Fri Aug 15 16:07:43 CEST 2008

Thanks for the reply Justin 
I tried like this 
do_dssp -f .xtc -s .tpr -n .ndx -map str.map -o str
it has given 
Fatal error:
DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)

I checked with archives do_dssp is a seperate program and install separately, 
Could you pls tell me how can I install do_dssp program or is there anyway to calculate  secondary structure of protein?
Thanks in advance. 

On Fri, 15 Aug 2008 Justin A.Lemkul wrote :
>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 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.
>>>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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