AMBER Archive (2006)

Subject: Re: AMBER: problem in calculating EGB using sander for ligand containing F atom

From: David A. Case (
Date: Thu Nov 09 2006 - 10:14:06 CST

On Wed, Nov 08, 2006, VANDANA KUMARI wrote:

> I am calculating EGB of my ligands using sander. I have
> done it successfully for some of my ligands but I am having problem with
> ligands containing F atom. whenever I am running sander message is
> comming "bad atom name F". I also tried to add library in
> ions94.cmd and ions94.lib. but still my problem persists. same error
> message is comming. What should i try for running sander for ligands
> containing flourine atom?

We need more information from you:

What is the exact error message? What you list above doesn't seem to be an
Amber error message.

What version of sander are you using?

Did you set gbsa to a non-zero value?

In general, providing more context about what your input and output was would
be helpful.


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