AMBER Archive (2007)

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

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Oct 25 2007 - 01:54:33 CDT

Quoting David Mobley <dmobley_at_gmail.com>:

> 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?)

In the R.E.D./R.E.DD.B. strategy:
- You build PDB file(s) in XLEaP
- You run Ante-RED to get P2N file(s) + Gaussian/GAMESS/PC-GAMESS output files
- You run R.E.D. to get Tripos mol2 file(s) or FF library precursor(s)
=> The data generated by R.E.D. are compatible with a project ready to
be submitted in R.E.DD.B.
- You load the Tripos mol2 file(s) into LEaP using scripts
  (in such a script you provide FF atom types, missing FF parameters;
all that can not be contained in a FF library precursor such as the
Tripos mol2 file format)
=> New LEaP commands are now available (if needed)
- You generate your OFF FF library(ies) -or prepin; whatever...- and
your prmtop/prmcrd files for MD simulation

The _key_ starting point is the P2N file:
see http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3
Two columns of atom names:
* The 1st one to define the equivalencing procedure during the charge
fit; i.e. in short to define the charge values
* The second one to define the atom names of the _future_ FF library
(Tripos, then OFF and then prmtop...)

For a MiniHowto, see also
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#1

I hope this helps,
regards, Francois

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