Re: AMBER: prepin file format description; pointers on parameterization

From: FyD <>
Date: Thu, 25 Oct 2007 07:27:33 +0200

Quoting David Mobley <>:

> I have a further follow-up question, because it dawned on me that all
> you've been telling me about is how to set up a heme by itself. Since
> I have a heme in a protein, setting up a heme by itself won't
> necessarily solve my problem.


> In particular, I need to get to the point where I can load something
> into leap, then load a PDB containing a heme, and get out proper
> parameters. Presumably the prepin file for heme that is distributed
> with AMBER is set up to tell tleap how to recognize that the heme is
> bonded to HIS (after I rename HIS in a pdb file, that is). If that's
> the case, I don't see how all of the information contained in this
> prepin file could possibly be stored to a mol2 file. (If so, how?)

You have tutorials for that.

You have the AMBER and tutorials for that.
And see what is a force field library and to load it in LEaP

regards, Francois

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Received on Sun Oct 28 2007 - 06:07:17 PDT
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