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

From: FyD <>
Date: Wed, 24 Oct 2007 21:09:09 +0200

Quoting David Mobley <>:

> 1) Can anybody point me to a description of the "prepin" file format
> (i.e., the format used by, or, 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.

Did you look in plep; see "Old Prep/Link/Edit/Parm Also Spasms, a
molecular dynamics program, and Resp, for charge-fitting. Resp Q&A" on
the AMBER web site.

Even reading what you report below, I still do not understand very
well why you do want to use the old prepin file format since it should
be possible to convert this file format into either mol2 file format
or OFF force field libraries.

For mol2 file format you could see the following pages:
and in particular:
  -I.3.3- The Tripos mol2 file format .
Please, see also the new "savemol2" command incorporated in LEaP
  -I.3.3.5- Using Tripos mol2 files in LEaP: Implementation of new
features in LEaP .

> 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

Looking for heme from the J. Comput. Chem. web site gives:

In particular, you could look at:
Classical force field parameters for the heme prosthetic group of cytochrome c
Journal of Computational Chemistry
Volume 25, Issue 13, Date: October 2004, Pages: 1613-1622
Felix Autenrieth, Emad Tajkhorshid, Jerome Baudry, Zaida Luthey-Schulten

Read the last paragraph about RESP charge derivation, & you will see
it is tricky on heme.

In this paper, the authors compute RESP charges for the heme + _all_
the ligands. The tricky point is to get a correct minimum with a
correct QM packages and to get SCF convergence for the correct spin
multiplicty/electronic configuration... You might look at the Jaguar
package to save you a lot of Gaussian/GAMESS cpu time ;-)

Finally, I think heme electronic configuration is highly depend on the
ligands. Thus, you should think about deciding or not deciding to
remove ligands from the whole heme system in your QM computation...

> 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.

My understanding is that antechamber does not work with metals yet.

regards, Francois

PS We will release a general heme force field in R.E.DD.B.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Oct 28 2007 - 06:07:12 PDT
Custom Search