> I wonder if anyone knows how to extract the residues of first solvation shell
> from the simulated system after the production?
>
> My system contains a host, guests, solvent, I want to get the information
> (prmtop or pdb) of the residue groups in the first solvation shell for the
> mm_pbsa study. I wonder if there is a quite way to do that cause i have so
> many snapshots. The only thing i can find in the manual is "watershell", but
> it only give the number of residue included in the shell.
The closest option will do this, saving the "n" number of solvent
molecules closest to the solute of interest. If your solvent is residues
named ETH and you want to save the closest 20 waters around residues 1-3,
trajin mdcrd.1
trajin mdcrd.2.gz
trajout mdcrd_20closest.trj
solvent byname ETH
center :1-3 mass origin
image origin center familiar
closest 20 :1-3 first noimage
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Received on Tue Nov 22 2005 - 04:53:02 PST
