AMBER Archive (2005)

Subject: AMBER: Re: R.E.D. question

From: FyD (fyd_at_u-picardie.fr)
Date: Fri Apr 29 2005 - 15:21:34 CDT

Quoting Yanze Zhang <yz.zhang_at_gmail.com>:

> I am a RED new user. I posted this question in AMBER forum but I think maybe
> I can directly ask you such a question.

Yes, please ask your future questions in the AMBER mailing list

> I am trying to use RED to test RESP charges on some peptides to see if
> it will reproduce the charges assigned on atoms in amino acids in
> AMBER library.

I do NOT think you will be able to reproduce the charges available in the AMBER
DB. See the FAQ on the R.E.D. web site why...
http://www.u-picardie.fr/labo/lbpd/RED/FAQ-I.htm#4 and other FAQ
It is the reason why we implemented multi-orientation RESP fit in R.E.D.-I

> Because when I only use Gaussian and "antechamber" in AMBER I can't
> get good agreement.

That has nothing to do with "antechamber". It is just that many thinks can
affect charge value accuracy:
- accuracy of the opt. geometry
- molecular orientation of the optimized geomtry
- human errors since the procedure to derive RESP or ESP charges is error prone
- different (& incorrect) basis set used in geometry optimized (& MEP
computation)
etc...

> I ran Gaussian on a cluster, so I only did MEP & CHR in RED using the
> Gaussian output file.

Yes, you are right. I think it is the safest way to use R.E.D. in an 'automatic'
way since the Geom. opt. can fail because of missing to locate the minimum at
the demanded threshold...

It means you used:
$OPT_Calc = "Off";
$MEPCHR_Calc = "On";
[...]
$JOB_OPT = "./Gaussian-output-4-Geom-opt"

> But the error message said "Invalid Minimization OUTPUT".

R.E.D. checks:
1- The presence of the words "Normal termination of Gaussian" at the end of each
Gaussian job (Geom. opt. & MEP computation)
2- The presence of a "Standard orientation" found after the words "Stationary
point found" (Geom. opt. only)
3- The atom order in the 'initial' PDB file & in the Gaussian output loaded must
be _the same_.
If these conditions are not fullfiled, R.E.D. complains by "Invalid Minimization
OUTPUT" and stops the charge derivation procedure.

> The command I used in Gaussian gjf file is
> #p HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt
> Could you tell me what is wrong?

Only the following keywords are needed in Geom. opt.:
#p HF/6-31G* Opt=Tight Test
or better
#p B3LYP/6-31G* Opt=Tight Test

The MEP computation is performed in a 2nd step.

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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