Hi,
I'm not 100% sure, but I *think* the charmm velocity trajectory format
is the same as the coordinate format (people with more charmm
experience please correct me if I'm wrong). If this is the case, you
can treat it as a normal trajectory; use cpptraj/ptraj to read in the
DCD trajectory and write out the PDB files, but instead of coordinates
in the XYZ fields you will have velocities. Note that in cpptraj in
order to make separate PDB files you need to use the 'multi' keyword,
otherwise a single PDB file is written with frames separated by
MODEL/ENDMDL records.
Hope this helps,
-Dan
On Fri, Aug 9, 2013 at 7:05 PM, Ganesh Kamath <gkamath9173.gmail.com> wrote:
> Hi amber experts,
> I have binary velocity files from my charmm run. Is it possible to read
> them in ptraj and convert to pdb files with atoms having velocities.
> Any help will be greatly appreciated.
> Thanks,
>
> ganesh
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Sat Aug 10 2013 - 22:30:02 PDT
