Re: [AMBER] Atom name convention/conversion in antechamber

From: David A Case <>
Date: Tue, 29 Mar 2011 07:54:04 -0400

On Tue, Mar 29, 2011, wrote:
> this may be a stupid question, but what file format would you recommend to
> define a new residue for leap?
> What Ive done up to now is the sequence
> antechamber -> prepin file -> leap -> *.{crd,top}

I ususally use mol2 rather than prepin. It *should* minimize (eliminate?)
problems with atom-reordering, and lots of other programs can read and write
mol2 files. I think it doesn't encode "head" and "tail" atoms, so you might
need to add that to a leap script that loads such a modified residue.

This would be a good question to post to the mailing list, since you might
get a wider variety of suggestions.


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Received on Tue Mar 29 2011 - 05:00:06 PDT
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