VMD-L Mailing List

From: mashaojie163 (mashao_jie_at_163.com)
Date: Mon Oct 11 2004 - 01:30:48 CDT

Hi:
  you just using autoionize package.
  excute the commands,(suppose you require 10 Cl ions):
  
package require autoionize
 autoionize -psf mypsf.psf -pdb mypdb.pdb -nna 0 -ncl 10 -o prefix

----- Original Message -----
From: "Cetin Baloglu" <cetinb_at_su.sabanciuniv.edu>
To: <namd-l_at_ks.uiuc.edu>
Sent: Monday, October 11, 2004 12:51 PM
Subject: namd-l: counterion software

> Hi,
> I want to add some amount of chloride as counterion to my protein file,
> before running with namd. To be more effective , I don't want to do it
> manually. There is a program for that purpose on site ,unfortunately it
> works only for sodium ion. I checked the C file, but couldn't find the
> variable to change sodium ion charge so as to mimick a negative ion. Can
> you offer me a script or a small program for that purpose.
>
> thanks in advance.
> Cetin Baloglu
>