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

From: David Mobley <>
Date: Thu, 25 Oct 2007 13:41:06 -0700


> 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

If I had wanted to use RED to do this, I would have asked how to do
that originally. The reason I'm e-mailing the AMBER e-mail list and
asking questions about AMBER is I wanted to know how to do it using
AMBER tools.

Best wishes,
The AMBER Mail Reflector
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Received on Sun Oct 28 2007 - 06:07:26 PDT
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