AMBER Archive (2005)

Subject: Re: AMBER: RED question

From: FyD (fyd_at_u-picardie.fr)
Date: Sun Jun 26 2005 - 22:37:59 CDT

Quoting Kara Di Giorgio <kdigiorgio_at_sbcglobal.net>:

> I'm working through the RED tutorials in the version 1 manual. I think
> I understand modifying the RED.pl file.
> I'm not sure HOW the data is
> output (what format) and where to find it (this isn't mentioned in the
> manual).

The 'final' output is a Tripos .mol2 file. See for instance the fig 1 page 4
However, the R.E.D.-I manual was 'a' 1st version. I think the manual of
R.E.D.-II should be more clear...

> I'm using g03 on a sunray system. Also, how do you use the
> output info from RED with antechamber?

The charges (taking into account several conformations & orientations) derived
by R.E.D. are available in a Tripos file...

You can load a Tripos file (instead of a prep.in file) in LEaP...

# load the Mol_o.mol2 Tripos file
MOL = loadmol2 Mol_o.mol2
# Save into an OFF LEaP library
saveoff MOL MOL.off

Regards, Francois 

-- 
  F.-Y. Dupradeau
DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
The Scripps Research Institute, La Jolla, CA, USA
       --
http://www.u-picardie.fr/labo/lbpd/FyD.htm
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