AMBER Archive (2009)

Subject: Re: [AMBER] test charge

From: Dan Kaps (
Date: Thu Feb 19 2009 - 20:22:31 CST

The command was as follows
antechamber -fi .pdb -fo prepin -i file.pdb -o file.prepin -at gaff -pf y -j 0 -c bcc -nc 1
(i don't quite understand why -nc is one but thats the only way it runs at all) Sorry for not being completely amber-literate, I am actually a physicist using this for an apparently unorthodox application. I also tried using an water molecule as well; however, the water molecule dissapeared in the .prepin file and was replaced by three "X" with "nan" as coordinates. Let me know if there's anything else I left out.
Dan kaps

From: David A. Case <>
To: AMBER Mailing List <>
Sent: Wednesday, February 18, 2009 11:24:04 PM
Subject: Re: [AMBER] test charge

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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