Re: AMBER: problem regarding water handling in explicit simu

From: Mingfeng Yang <>
Date: Fri, 30 Mar 2007 12:50:00 -0700

On Fri, 2007-03-30 at 15:05 +0530, gurpreet singh wrote:
> hello Amber users
> i musing Amber 9 for carrying an explicit simulation i want to ask two
> questions:
> 1) i want to remove a particular water molecule from my ongoing
> simulation , how can i make the corresponding topology file ie
> topology file with that water removed, and how can i get the
> corresponding restart file with all the velocity information intact
> but with removal of information related to that particulat water
> molecule
> i can use ptraj strip command but that usually dont give the velocity
> information in the output file we got from it
It seems ptraj has an experimental function which can rebuild topology
after stripping certain atoms out. But I am not sure if it works or not.

A simple way is to recreate topology file with a PDB file containing no

> 2) if i want to restrict the water molecules to reach a particular
> area in the protein then is their any way in amber by which i can
> create this type of potential barrier so that water or any solvent
> molecule dont come near that place

Probably you can use distance constraints.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Apr 01 2007 - 06:07:45 PDT
Custom Search