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

From: FyD <>
Date: Wed, 24 Oct 2007 22:13:37 +0200

Quoting David Mobley <>:

> 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).

I wonder if the AMBER 5 manual there were tutorials about plep...

> 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.

Instead of editing, you could also use LEaP scripts to add the
information required to construct a FF library.
You could study the LEaP script for 10 solvent (whole) _molecules_ at:
You could study also this other one for 32 DNA/RNA _fragments_:

> I guess as you're suggesting perhaps I can just read it into leap and
> save it as a mol2.

Yes, for instance.
However, in your case because I guess you will have to handle
molecular fragments the best bet might be to use the OFF format since
it can contains information about connecting atoms between fragments.
Or you could use mol2 files as FF precursors for OFF FF libraries. It
is the strategy used in R.E.D./R.E.DD.B. ;-)

> 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?

prepin, mol2, OFF and RTF (CHARMM) are only FF libraries. More or less
the same. Please, read the Tripos mol2 description in the tutorials: you will find information about FF

>> 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.

Instead of histine, just used Me-Imidazole and set an Intra-molecular
charge constraints (INTRA-MCC) on the Methyl using R.E.D.: This is

> 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.

For sure R.E.D. will do the job ;-)

regards, Francois

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Received on Sun Oct 28 2007 - 06:07:13 PDT
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