[AMBER] request for help in water shell and closest command

From: Robin Jain <robinjain.chem.gmail.com>
Date: Mon, 30 Dec 2013 12:13:57 +0530

Dear amber users,
 1. I am doing solvation of a organic molecule containing carbonyl group
in 437 methanol. Now i want to calculate the closest 64 methanol molecule
to my solute. I tried for this using ptraj and generate a pdb file but on
using VMD i found that some methanol molecule are more far to solute,.what
skould i do. i used the script as follows-

*trajin xyz.mdcrd 1 1000 1*

*trajout xyz.pdb pdb*

*solvent byname MOH*
*closest 64 :1*

2. An another problem is that i want to view the first and second
solvationshell. for this purpose i used watershell command in ptraj
and get a output
with 3 column. what should i do further for visulization.

Please help me.

Thanking You.
Robin Jain
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Received on Sun Dec 29 2013 - 23:00:02 PST
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