AMBER Archive (2000)

Subject: Re: modify topology file

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Fri Jun 23 2000 - 18:51:53 CDT

> i've a topology file for a dna with ions and water. i want to
> get a new topology file for the dna without water and ions. i can
> strip the waters out using rdparm, i would like to know if there is
> any way to strip all the ions.

May be easiest to make a new topology file: delete the waters &
ions from a pdb; e.g. assuming the residue name is CIO:

% egrep -v 'WAT|CIO' file.pdb > newfile.pdb
% tleap
> x = loadpdb newfile.pdb
> saveamberparm x new.top new.crd
> quit

Bill Ross