Hassan Shallal wrote:
Dear Gromacs users,
I need trjconv to write me pdb files at a list of frames that are
randomly chosen throughout the whole production trajectory (they belong
to the least energetic 100 frames).
I can use trjconv to write a pdb at each frame but this is gonna be time
consuming, so I looked in the specifications of trjconv and found that
there is an optional input -fr frames.ndx, I guess this might be useful
for what I want but I am not quite sure how to write an index file for
randomly distributed frames points not
for atoms or residues, the command make_ndx doesn;t provide any options
for frames of time points!!
I tried to create an ndx file manually by writing the frames numbers in
a txt file, calling it frames.ndx, feed this to the -fr option of
trjconv, as I expected, trjconv dealt with
the numbers as numbers of atoms not of frames! How can I tell trjconv
that the numbers in frames.ndx file are actually numbers of specific
time points not of residues.
That's what it's supposed to do, so I'd suspect that there's something wrong
with your index file. If you want to write out frames 1 and 2, for instance,
your frames.ndx file should be something like:
[ frames ]
1 2
-Justin
Any help or hint is very appreciated..
Thanks alot
Hassan
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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