Re: AMBER: closest water molecules with 8 angstroms

From: Alessandro Nascimento <>
Date: Wed, 19 Dec 2007 08:49:56 -0200

You can use the command "watershell" in ptraj.
Take a look at the manual, but supposing your beta-cyclodextrine is the
first residue in your simulation file, you can use something like this:

ptraj myprmtop.prmtop << eof
trajin mymd.mdcrd
watershell :1 wshell.dat lower 3.5 upper 8.0

This will compute (and write to file wshell.dat) the number of water
molecules in the first and second solvation shell, which you can specify in
the input.
In the case above, I used 3.5 and 8.0 Ang within residue 1.

Hope this helps,


On Dec 19, 2007 4:52 AM, nag raj <> wrote:

> Dear Amber users,
> I solvated beta-cyclodextrine using TIP3P
> solvent box. In mdrun trajectory 80 conformations are saved. I want to know
> the number of water molecules within 8 angstroms to cyclodextrine (solute)
> in each conformation.
> I looked into the ptraj module, closest and solvent
> commands are giving number of water molecules as mentioned in input but not
> restricted to distances.
> Any suggestion is appreciated.
> with best regards,
> Nagaraja Mulpuri.
> ------------------------------
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Received on Sun Dec 23 2007 - 06:07:03 PST
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