AMBER Archive (2009)

Subject: Re: [AMBER] test charge

From: David A. Case (
Date: Thu Feb 19 2009 - 22:48:29 CST

On Thu, Feb 19, 2009, Dan Kaps wrote:

> 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.

As I said before, if you have a "real" closed shell molecule, this is
what antechamber is designed for. It won't handle "test charge"
hydrogens, and I'm not sure it will handle multiple molecules (e.g.
benzene + water). It's still not clear what you really want to do, but
it sounds like you are trying to make antechamber do something it was
not designed to do.

If you post the input pdb file, someone on the list might be able to say


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