Dear Dac,
Thank you very much Sir for your valuable reply. I changed the code as
suggested by you and it is working properly. Thank you once again!
On Mon, Sep 17, 2012 at 9:49 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Mon, Sep 17, 2012, Rajeswari A. wrote:
> >
> > I want to simulate a protein with inhibitor molecule. As the inhibitor
> > molecule is from the crystal structure, we thought to get only ESP
> charges
> > from Gaussian without any optimization (with POP=CHELPG). The log file of
> > our gaussian run completed successfully. The log file is attached for
> your
> > reference. When i feed this log file in antechamber, the produced prep
> file
> > is not taking the charges in gaussian log file, instead giving 0.0000. A
> > part of prep file is shown below.
> >
> > 0 0 2
> >
> > This is a remark line
> > molecule.res
> > IND INT 0
> > CORRECT OMIT DU BEG
> > 0.0000
> > 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
> > 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
> > 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
> > 4 C5 c3 M 3 2 1 1.540 111.208 180.000 0.000000
> > 5 H4 hc E 4 3 2 1.070 90.964 161.802 0.000000
> > 6 H5 hc E 4 3 2 1.069 150.095 27.478 0.000000
> > 7 H6 hc E 4 3 2 1.070 82.319 -88.649 0.000000
> > 8 C4 c3 M 4 3 2 1.546 41.376 42.779 0.000000
> >
> >
> > i run the antechamber with the following command.
> > antechamber -i gaussian.log -fi gout -o xxxx.prepin -fo prepi -c esp
> >
>
> This is a bug of sorts. A Gaussian output file might have several sets of
> Mulliken or esp charges in it. Junmei decided that the ones following a
> "Stationary point found" statement should be the ones to use. But this
> requires that an energy minimization have been performed, which is often
> not
> the case.
>
> The simplest workaround is to change the charge.c file in
> $AMBERHOME/AmberTools/src. Change line 229 to initialize Found_Stationary
> to 1 (rather than 0). Then type "make install" to recompile the program.
>
> Thanks for the report.....dac
>
>
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Received on Tue Sep 18 2012 - 01:00:03 PDT
