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 Mon Sep 17 2012 - 09:30:10 PDT
