AMBER Archive (2007)

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

From: David Mobley (dmobley_at_gmail.com)
Date: Wed Oct 24 2007 - 12:52:24 CDT

All,

I have several questions, and I begin with the most basic:

1) Can anybody point me to a description of the "prepin" file format
(i.e., the format used by all_amino94.in, or heme_all.in, for
example)? I can't find this on the file format description page, nor
in the manual, and I'm trying to figure out what the columns
represent.

At a more detailed level, the basic problem I'm trying to solve is
that I (to my chagrin) need to simulate an artificial mutant of
cytochrome C peroxidase, which has a heme (heme B, particularly)
bordering an artificial binding site I'm interested in. The chemistry
of the heme isn't particularly important here, but I do at least need
"sane" parameters for it so it stays stable, etc.

There are a set of heme parameters distributed with AMBER for heme,
apparently, and I hope to be able to modify them to describe my
particular case. They're originally for myoglobin/hemoglobin, if I
understand correctly, and are apparently for heme with the iron
covalently bound additionally to histidine and O2. In my particular
case, the iron should be covalently bound to histidine and a water
molecule. I'm trying to figure out how I need to modify the existing
parameters to achieve this (hence question #1).

This brings me to my follow-up question:

2) My rough idea of the procedure I need to use follows; is this
roughly right? (and any tips on how to accomplish the specific steps,
especially step (a), will be appreciated):
(a) Modify the existing heme parameters to get it to connect to water
(b) separately run QM at the appropriate level on the iron+heme
(without histidine/water, probably) and perform a RESP fit to get the
partial charges
(c) incorporate the partial charges into the parameter files
(d) Load the whole thing together with my pdb into leap somehow and
write out prmtop and crd files

Any general pointers on this will be greatly appreciated. I've used
leap/antechamber before for setting up normal proteins and
parameterizing small molecules that are non-covalently attached (i.e.
that can be done in the "normal" way through antechamber) so I'm
familiar with those "standard" steps, but am a bit at a loss when it
comes to how to set up and tweak nonstandard residues.

Thanks a lot,
David
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