I am using AMBER Tools 1.5.
the leaprc.amoeba in the $AMBERHOME/dat/leap/cmd/leaprc.amoeba give similar
issues as mentioned in the post (
http://dev-archive.ambermd.org/201103/0117.html). So I am using
leaprc.amoeba as included in AmberTools/test/sleap/amoeba/leaprc.amoeba
Your feedback is appreciated.
On 5 October 2011 00:05, case <case.biomaps.rutgers.edu> wrote:
> On Tue, Oct 04, 2011, Neha Gandhi wrote:
> >
> > I am now trying to follow tutorial on amoeba force field as mentioned on
> > http://bessie.che.uc.edu/wiki/AMOEBA.
> >
> > I m using AMBER11.
>
> sleap is a part of AmberTools: which version of that are you using?
>
> > I m attaching my protein file. The steps i followed is
> >
> > >sleap
> > >source leaprc.amoeba
> > This loads
> >
> > < loadoff amoeba_amino.off
> > < loadoff amoeba_aminont.off
> > < loadoff amoeba_aminoct.off
> > < loadoff amoeba_watbox.off
> > < loadamoebaparams amoebapro.prm
> >
> > >loadoff sys.off -> this is for chloride ion
> > m1=loadpdb phf6amber.pdb
> >
> > When I try to save parameters, it gives error: cannot find atom 75 in
> > molecule.
>
> It works for me, not giving any errors. I guess we need more details from
> you
>
> ....dac
>
>
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--
Regards,
Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845
Phone: 9266 9061
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Received on Wed Oct 05 2011 - 00:30:02 PDT
