AMBER Archive (2009)

Subject: Re: [AMBER] test charge

From: David A. Case (
Date: Wed Feb 18 2009 - 22:24:04 CST

On Wed, Feb 18, 2009, Dan Kaps wrote:

> Hi I am investigating the effects of a test charge (in this case simply
> a hydrogen atom) on a long chain of benzene rings. The test charge is
> placed directly above the center benzene ring. I am attempting to run
> the .pdb file through antechamber to get the .prepin file; however,
> I am having some difficulties. The .prepin file replaces the test
> charge with an "X." It literally just says "X" instead of H. Also, it
> replaces two of the spacial coordinates with "nan" not a number. Does
> anyone know what the problem is and how I can fix it?

We would need to know details of what you mean by "run the pdb file
through antechamber": what flags did you use? Note that antechamber (in
most uses) needs to have a chemically reasonable, closed shell
structure. It is designed to create force fields for "real" molecules,
and may indeed not work well for systems with a dangling hydrogen atom.
But without more details, its hard to be very helpful.


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