[gmx-users] Extract van der waals surface atoms coordinates

[Justin A. Lemkul]

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

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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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