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

From: Jason Swails <>
Date: Tue, 29 Mar 2011 08:46:23 -0700


As is the custom for online mailing lists, I'll toss in my comments here as
well, although your question has been answered for the most part.

I'll agree that mol2 files are preferable to prepins, but like Dave said,
mol2 files don't record head or tail atoms (so by default leap won't connect
it to any adjacent residues). My suggestion is to generate mol2 files, then
use those mol2 files to create an amber OFF (library) file. You can do this
through leap, and set the head and tail of your residue so that the OFF file
knows which atoms to bond to adjacent residues.

Another comment I'll make is in regards to your TI calculations. There's a
nifty little python program written by Thomas Joseph in
$AMBERHOME/AmberTools/src/etc/ that helps automate the
procedure a little bit. I'm not *exactly* sure how it works, but if you
play around with it a little bit (and read through the code some), it's
probably fairly easy to figure out. It'll probably make softcore
simulations easier in the long run.

Hope this helps,

On Tue, Mar 29, 2011 at 4:54 AM, David A Case <>wrote:

> 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.
> ...dac
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Tue Mar 29 2011 - 09:00:02 PDT
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