On Wed, Oct 05, 2011, Neha Gandhi wrote:
> 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).
Yes I can see this problem, too. I'm cc-ing this to Wei, to see if he can
find the problem.
So I am using
> leaprc.amoeba as included in AmberTools/test/sleap/amoeba/leaprc.amoeba
> > >
> > > >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.
The only difference for me is that I am not loading the sys.off file (which is
not needed for this test case.) Can you try to leave out that step? Also,
it's not completely clear what you mean when you say "try to save parameters":
was this before or after adding water (and/or chlorides)? Please continue to
give the *exact* commands you used. As I said, it works for me, but I have
to make guesses or assumptions about what you really did.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 06 2011 - 07:30:03 PDT
