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

From: David Mobley <>
Date: Wed, 24 Oct 2007 16:58:35 -0700

Hi again,

On 10/24/07, FyD <> wrote:

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?)

This is why I wanted to understand the prepin format to begin with,
but so far I've gotten no pointers in that direction. Again, is this
documented somewhere?

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Received on Sun Oct 28 2007 - 06:07:15 PDT
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