From: mashaojie163 (mashao_jie_at_163.com)
Date: Mon Oct 11 2004 - 01:46:24 CDT
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
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