Prof Case
The command we gave is
antechamber -i x.log -fi gout -o x.prep -fo prepi -c esp -s 2
The prep file generated has parameters for boron (our molecule is BF4) but
the values against fluorine say 'nan'.
We need the prep file because we will be generating an frc file with
parameters taken from literature and not the ones in Amber library.
Thanks
On Wed, Jan 29, 2014 at 8:57 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Wed, Jan 29, 2014, DEBOSTUTI GHOSHDASTIDAR wrote:
> >
> > I have calculated esp charges for BF4 using gaussian G09.While converting
> > the log file to the prep file using antechamber, the Fluorine atoms are
> not
> > being recognized and NEWPDB is empty.
>
> 1. Can you give the exact command-line arguments you are using?
> 2. What makes you conclude that the fluorine atoms are not being
> recognized?
>
> > The log file and the corresponding mol2 file are fine
>
> If the "mol2 file is fine", can you not use that? NEWPDB is just an
> intermediate file in any case. If you have the mol2 file, you should be
> good
> to go.
>
> I'm probably not understanding what you did, and what exactly went awry.
>
> ...dac
>
> >
> > Running: /usr/local/bin/amber12//bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> > ANTECHAMBER_AC.AC -p gaff
> >
> > Running: /usr/local/bin/amber12//bin/prepgen -i ANTECHAMBER_PREP.AC -f
> int
> > -o BF4_ani.prep -rn "MOL" -rf molecule.res
>
> p.s. Note that antechamber doesn't know anything about boron. You'll have
> to
> generate parameters for that on your own (or follow the instructions in
> section 2.2 of tutorial A15.)
>
>
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>
--
Debostuti Ghosh Dastidar
PhD Scholar
Computational Biophysics Lab
Department of Biotechnology
Indian Institute of Technology Madras
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Received on Wed Jan 29 2014 - 21:00:02 PST
