AMBER Archive (2007)

Subject: Re: AMBER: problem regarding water handling in explicit simu

From: Mingfeng Yang (mfyang_at_gmail.com)
Date: Fri Mar 30 2007 - 13:50:00 CST

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
water.

> 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.

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