AMBER Archive (2008)

Subject: RE: AMBER: RED III execution problem

From: ben rodriguez (bramber_at_live.com)
Date: Mon Jul 07 2008 - 14:21:11 CDT

Thanks for the reply, RED is now working. I also have optimization output from Spartan (Windows) and would like to use them with RED to create libraries for Amber. I have looked at babel/openbabel, but writing to gamess output is not supported. Is there a way to use Spartan output with RED, or is there a better way to create the Amber libraries from the Spartan output.

Thanks,

Ben

> Date: Thu, 3 Jul 2008 11:25:24 +0200
> From: fyd_at_q4md-forcefieldtools.org
> To: amber_at_scripps.edu
> Subject: Re: AMBER: RED III execution problem
>
> Quoting ben rodriguez <bramber_at_live.com>:
>
> > I am trying to generate RESP charges using RED III, and GAMESS. I
> > get this error from the RED log file:
> >
> > CHARGE TYPE = RESP-A1
> > ---------------------------
> >
> > ===========================================================================
> > ======================= Single molecule ===========================
> > The molecule TITLE is "HOP"
> > The TOTAL CHARGE value of the molecule is "0"
> > The SPIN MULTIPLICITY value of the molecule is "1"
> > ===========================================================================
> >
> > Unknown output detected !
> > Invalid optimization OUTPUT !
>
> So far, R.E.D.-III only recognizes geometry optimization outputs
> generated from the Gaussian (94, 98, 03), GAMESS-US or PC-GAMESS
> programs.
>
> Using those programs, this "Invalid optimization OUTPUT" can have
> three origins:
>
> -1 The QM job generated is not valid. It did not finish correctly:
> check the following words in the Gaussian/GAMESS output:
>
> Gaussian:
> Author names
> ...
> Stationary point found
> ...
> Standard orientation
> ...
> Normal termination of Gaussian => Correct job
>
> GAMESS:
> Author names
> ...
> EQUILIBRIUM GEOMETRY LOCATED
> ...
> EXECUTION OF GAMESS TERMINATED NORMALLY => Correct job
>
> -2 The atom order in the .p2n file is not the same than that observed
> in the "Standard orientation" (after the "Stationary point found"
> words) [Gaussian], or after the "EQUILIBRIUM GEOMETRY LOCATED" words
> [GAMESS/PC-GAMESS].
> => rebuild your p2n file according to the atom order found in the QM output.
>
> -3 You have a frequency job in the Gaussian output. In this case, just
> remove this 'second' QM JOB1b (because of the "Freq" keyword):
>
> "JOB1" for gaussian with such a route "Opt=Tight Freq"
>
> "JOB1a" geometry optimization
> ...
> Stationary point found
> ...
> Standard orientation
> ...
> Normal termination of Gaussian
> "JOB1b" frequency calculation |
> ... |
> Standard orientation | removed this part
> ... | with a text editor
> Normal termination of Gaussian | from the ouput
>
> In this third case, see
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#6 ; In the
> section "-4", it is written:
>
> " Finally, the frequency job available in the Gaussian output has to
> be removed from the QM output (R.E.D. II and III only recognize
> optimization output, and generates an error message if an optimization
> job followed by frequency calculations is used as input; this might be
> changed in R.E.D. IV)."
>
> regards, Francois
>
> PS Please, check the bug fix on the R.E.D. web site...

_________________________________________________________________
It’s a talkathon – but it’s not just talk.
http://www.imtalkathon.com/?source=EML_WLH_Talkathon_JustTalk
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu