Thank you for your help!
Shuting
Quoting Thomas Cheatham <cheatham.chpc.utah.edu>:
>
> > 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 - 15:53:01 PST
