AMBER Archive (2007)

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

From: David Mobley (dmobley_at_gmail.com)
Date: Wed Oct 24 2007 - 14:31:02 CDT

Hi,

> > 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.
>
> 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.

That doesn't appear to be useful for my purposes; I'm trying to
develop all atom parameters, not edit united atom parameters (which is
what the README says that does).

> 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.

I don't care what file format I use. I'm just trying to figure out how
to use the files that are provided with the distribution (which are in
prepin format), i.e., first I need to know how to interpret them
myself so that I can edit them. Alternatively, if there's a tool I can
use to convert them to some other format that would be easier for me
to edit myself, that's great. All I need is (a) the files in some
format I can understand and edit, and (b) to be able to read it into
leap to describe the residue.

I guess as you're suggesting perhaps I can just read it into leap and
save it as a mol2. I just wasn't sure exactly what information is in
the prepin file since the file format isn't described anywhere;
looking at it it seems to contain information about bond angles and
such, which made me think it might contain more info than a mol2 file.
I take it you're saying this is NOT the case?

> 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

Yes, I've been looking at that paper.

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

Right. It has apparently been done before though.

> 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 ;-)

Yeah, I am indifferent as to package -- it'll either be GAMESS or Jaguar.

> 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...

Right, although then I guess I have to truncate the ligands, or at
least the histidine.

> > 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.

I know. I was just saying that I know how to use antechamber to do
"ordinary" ligands; I just don't know how to do parameterizations that
don't involve antechamber.

Thanks,
David
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