[AMBER] problem during add ions

From: Sohag Biswas <cy13p1001.iith.ac.in>
Date: Mon, 9 Jun 2014 15:51:02 +0530

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.
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Received on Mon Jun 09 2014 - 03:30:02 PDT
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