AMBER Archive (2005)

Subject: Re: AMBER: RED question

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Mon Jun 27 2005 - 00:13:13 CDT

Thank you for your quick response. I really appreciate all of your
help.

Kara Di Giorgio

On Jun 26, 2005, at 8:37 PM, FyD wrote:

> 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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