Hi,
I have two Questions relating to Ptraj errors:
A.
I have performed series of MD simulations on my protein system and
have bunch of .trj files. These .trj files were generated by using the
.rst file from the previous run respectively.
When I try to run ptraj with the following script, I don't get any
meaningful trajectory (instead its bunch of lines all over the place):
trajin 1.trj 1 10000 100
trajin 1b.trj 1 10000 100
trajin 1c.trj 1 10000 100
trajin 1d.trj 1 10000 100
strip !.CA
image origin center familiar
reference refh.pdb
rms reference
matrix covar name mcovar
analyze matrix mcovar out eveccc.pev vecs 25
trajout out.trj
My expectation is to get an out.trj which has just CA over the entire
time frame. But this is certainly not working for me. Any pointers on
where I could be wrong would be greatly appreciated.
B.
Similar to above I have .trj file on a protein DNA system. I have set
iwrap=1 in the input file for the simulation. After couple of runs,
what I observe is that one of my DNA strands have shifted. It
certainly has not dissociated as evident from the .trj file.
My thought is that it has moved to its image cell. My question is that
how can I restore my .trj file? How can I image the drifted DNA strand
back into the structure. I have used image origin center familiar in
Ptraj and can't get it to work. When I couple this command with
multiple trajin's again all I get is a bad output .trj file. Not sure
where things are getting weird.
Thanks in advance.
Best, AJ
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Received on Wed Oct 06 2010 - 12:00:03 PDT
