[gmx-users] Extract van der waals surface atoms coordinates
Justin A. Lemkul
jalemkul at vt.edu
Fri Nov 18 16:58:50 CET 2011
Alex Jemulin wrote:
> Dear All
>
> How can I extract van der waals surface atoms coordinates from MD
> Trajectory and write them to a file?
> Is it possible with gromacs? And with other tools?
g_sas -i produces a topology of surface atoms, from which you can get atom
numbers, create an index file, then use g_traj to extract the coordinates of
those atoms.
-Justin
--
========================================
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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