I have like five mol2 files which corresponds to the different conformations that I used I guess ...
/Urszula
________________________________________
Von: Per Jr. Greisen [pgreisen.gmail.com]
Gesendet: Freitag, 20. April 2012 10:04
An: AMBER Mailing List
Betreff: Re: [AMBER] P2N file error from RED
Dear Urzula,
Not an expert on this but have a look in the mol2 file this normally
contains the charges. It is normally the 9. column.
Hope this helps
On Fri, Apr 20, 2012 at 9:57 AM, Urszula Uciechowska <
urszula.uciechowska.chem.umu.se> wrote:
> Dear Fracois,
>
> I finally could run the RED without getting any errors. I had like 5
> conformations in the P2N file and now I dont know which file represents the
> final geometry with the resp charges?
>
> /Urszula
> ________________________________________
> Von: FyD [fyd.q4md-forcefieldtools.org]
> Gesendet: Dienstag, 17. April 2012 15:37
> An: AMBER Mailing List
> Betreff: Re: [AMBER] P2N file error from RED
>
> Dear Urszula,
>
> You have a +1 formal charge on the NH3+ group of the side chain of
> your pseudo lysine...
>
> So set REMARK CHARGE-VALUE to "1" in your P2N file.
>
> regards, Francois
>
>
> > I have prepared my p2n file and sent to RED IV. I got this error:
> >
> > WARNING:
> > Gaussian outputs generated by R.E.D. Server are stripped by R.E.D. IV
> > (in agreement with Gaussian Inc.)
> > Only pieces of information related to charge derivation
> > are conserved in the Gaussian outputs.
> >
> > g09 [
> OK ]
> > resp [
> OK ]
> >
> >
> > The Scratch directory defined for Gaussian is
> > /tmp/R.E.D.IV-8920.master0.q4md-forcefieldtools.org
> >
> > Scratch directory for Gaussian [
> OK ]
> >
> >
> > Geometry optimization(s) is/are being computed for molecule 1 ...
> >
> > Conformation 1 ... [
> FAILED ]
> > See the file(s) "JOB1-gau_m1-1.out"
> >
> > Check the total charge and spin multiplicity in your P2N file!
> >
> >
> >
> > Execution time: 0 h 0 m 1 s
> >
> > My p2n file is attached. What should I include more in p2n file?
> >
> > Thank you for any advise
> >
> > /Urszula
>
>
>
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--
Per
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Received on Fri Apr 20 2012 - 01:30:05 PDT
