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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