Hi Junmei,
Thank you for your help. The ANTECHAMBER_AM1BCC.AC files are consistent
with the prepc files, but the strange thing is that if I keep those files
in the directory and run both commands one after the other I get the same
charges, depending on what the AC files say. However, I run gaff2 first and
I got the igp_gaff2 charges. I kept files and run immediately gaff and got
the same gaff2 charges. Then I clear all those intermediate files and run
gaff and I get the igp_gaff charges. I hope my explanation it's not too
confusing, What I am trying to figure out is, if I have those intermediate
AC files in the directory and I run antechamber, could it be reading
directly those in the current directory and thus producing consistent
charges with the last run, and then if I clear the intermediate outputs
reads the AC files in $AMBERHOME.
Thanks again for your help.
Yuliana
On Mon, Jul 30, 2018 at 12:50 PM, Junmei Wang <junmwang.gmail.com> wrote:
> 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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> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > >
> > >
> > > --
> > > Yuliana Bosken
> > >
> >
> >
> >
> > --
> > Yuliana Bosken
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
--
Yuliana Bosken
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Received on Mon Jul 30 2018 - 13:30:02 PDT
