try the following:
addions pdb Na+ 2
On Mon, Jun 9, 2014 at 12:21 PM, Sohag Biswas <cy13p1001.iith.ac.in> wrote:
> dear amber user,
> i want to neutralise my system with 2 Na+ ions. My system contains 2 SO42-
> and 100 wat.
> For that following command i am using.
>
> tleap -s -f leaprc.gaff
> > loadamberprep sulfate.prepi
> > loadamberparams sulfate.frcmod
> > loadamberprep wat.prepi
> > loadamberparams wat.frcmod
> > pdb = loadpdb sul-100wat.pdb
>
> and for adding two Na+ i am using following commands
> addIons2 pdb Na+ 0
>
> but it is not working. How to solve this problem??
> Many many thanks in advanced.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Senior Lecturer (Organic Chemistry)
School of Chemistry and Physics
University of Kwa-Zulu Natal (UKZN)
Westville campus
Durban, South Africa
email: singhp4.ukzn.ac.za, parveshdurban.gmail.com
Phone: +27-31-2602181 (o), +27745147754 (m),
web: http://chemistrywst.ukzn.ac.za/HomepageW.aspx
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 09 2014 - 07:30:02 PDT
