<P>
<BR>
Thanks for the reply Justin <BR>
I tried like this <BR>
do_dssp -f .xtc -s .tpr -n .ndx -map str.map -o str<BR>
it has given <BR>
Fatal error:<BR>
DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)<BR>
<BR>
I checked with archives do_dssp is a seperate program and install separately, <BR>
Could you pls tell me how can I install do_dssp program or is there anyway to calculate secondary structure of protein?<BR>
Thanks in advance. <BR>
<BR>
<BR>
On Fri, 15 Aug 2008 Justin A.Lemkul wrote :<BR>
><BR>
>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.<BR>
><BR>
>-Justin<BR>
><BR>
>Justin A. Lemkul wrote:<BR>
>><BR>
>><BR>
>>minnale wrote:<BR>
>>> Hi all,<BR>
>>> 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.<BR>
>><BR>
>>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.<BR>
>><BR>
>>Hence the lovely plots you see in the literature.<BR>
>><BR>
>>-Justin<BR>
>><BR>
>>>I am bit confusing with about do_dssp command.<BR>
>>>Can you explain me clearly. Thanks in advance.<BR>
>>><BR>
>>><BR>
>>><BR>
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>>><BR>
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><BR>
>-- ========================================<BR>
><BR>
>Justin A. Lemkul<BR>
>Graduate Research Assistant<BR>
>Department of Biochemistry<BR>
>Virginia Tech<BR>
>Blacksburg, VA<BR>
>jalemkul[at]vt.edu | (540) 231-9080<BR>
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>
><BR>
>========================================<BR>
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