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

From: FyD <>
Date: Mon, 02 May 2005 21:53:35 +0200

Quoting Yanze Zhang <>:

> 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".

Yes, the set of Cart. coordinates available after "Input orientation" is NOT
Only the set of Cart. coordinates available after "Normal termination of
Gaussian" & "Standard orientation"
is used by R.E.D. as input for MEP computation and/or rigid body re-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".

NO not closely.

> 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?

Yes please send me your Gaussian ouput and initial PDB file.

Regards, Francois

  F.-Y. Dupradeau
DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
The Scripps Research Institute, La Jolla, CA, USA
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Received on Mon May 02 2005 - 21:53:00 PDT
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