AMBER Archive (2005)

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

From: Yanze Zhang (yz.zhang_at_gmail.com)
Date: Mon May 02 2005 - 14:19:14 CDT

Dr. Dupradeau,

Thank you for explaining things again and again for R.E.D. new users like me.
But I have another question on the possible cause of "Invalid
Minimization OUTPUT" error. I checked the Gaussian output file, and I
found the word "Normal termination of Gaussian" , and also "Standard
orientation" after the words "Stationary point found", but that is
after several lines which have a title "input orientation". I wonder
if you mean the "Standard orientation" should be the words following
"Stationary point found" closely or it can be whereever after the
"Stationary point found". If it is the former case I don't think the
program will ever work because this is not consistent with the
Gaussian03 output. I also checked the atom order in pdb file and
Gaussian output file, and they are the same. So I am really confused
what is wrong. Could you give me some clue? Can I send my Gaussian
output file and pdb file to you to if possible?

Thanks.

Regards,
Yanze

On 4/29/05, FyD <fyd_at_u-picardie.fr> wrote:
> 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
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu