Hi Yuliana
I have tested you molecule and run the same commands with different
versions of AMBER packages including Amber18. I got identical prepc files
for "-at gaff" and "-at gaff2", which is also identical to your
igp_gaff.prepc. Could you check if the two intermediate files are the same:
sqm.out and ANTECHAMBER_AM1BCC.AC?
All the best
Junmei
On Mon, Jul 30, 2018 at 2:16 PM, Yuliana Bosken <ydavi002.ucr.edu> wrote:
> Hi Dr. Case,
> I was wondering if you had a chance to look at my mol2 and my prepc files?
> I am still not sure if I am doing something wrong when generating those
> prepc files.
> Thanks,
> Yuliana
>
> On Sun, Jul 29, 2018 at 10:23 AM, Yuliana Bosken <ydavi002.ucr.edu> wrote:
>
> > Hi,
> > Thank you for your reply. Attached are the mol2 file and the two versions
> > of prepc file that I get. We use Amber16 and AmberTools16, I may have
> > upgraded to AmberTools 17 on one of the computers I am using but I am not
> > quite sure and I don't know how to check the version.
> > Thank you,
> > Yuliana
> >
> > On Sun, Jul 29, 2018 at 5:13 AM, David A Case <david.case.rutgers.edu>
> > wrote:
> >
> >> On Sat, Jul 28, 2018, Yuliana Bosken wrote:
> >>
> >> > I used antechamber to generate charges for my ligand. However, for
> some
> >> > reason when I select gaff for atom type I get different charges than
> >> gaff2.
> >> > Is that normal or I am doing something wrong?
> >>
> >> Thanks for the report.
> >>
> >> Can you post the igp.mol2 file you are using as input, so we can explore
> >> this behavior? (I could convert prepc files, but you only gave a part
> >> of the prepc file, so it would be best to make sure I'm using the same
> >> inputs that you are.)
> >>
> >> Also, please let us know which version of AmberTools you are using.
> >>
> >> ...regards...dac
> >>
> >>
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> >>
> >
> >
> >
> > --
> > Yuliana Bosken
> >
>
>
>
> --
> Yuliana Bosken
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Received on Mon Jul 30 2018 - 13:00:02 PDT
