Dear Prof.Case,
thanks for posting the reply.
Yes, the program sleap works find if I try to use saveamoebaparm and save
the parameters only for proteins. But when I try to combine chloride ion and
water with peptide, it doesn't work. I also wrote to Prof. Rogers who wrote
the tutorial for anions using amoeba force field. His reply is below:
Thank you for your kind attention,
Regards,
Neha
David Rogers wantye.gmail.com to me
show details 6 Oct (1 day ago)
I never got the thing to work with proteins, I was interested in
working from the basic amoeba forcefield parameters (which have also
changed since that tutorial was written to add variable Thole damping
parameters for multivalent cations) and so had to do extra work to
generate the prm file from those. The basic parameters come with the
Tinker program and have different atom type numbers. Let me know if
you find a better tutorial for working with amoeba+protein systems.
~ David Rogers
On 6 October 2011 22:06, David A Case <case.biomaps.rutgers.edu> wrote:
> 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
>
>
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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 Thu Oct 06 2011 - 19:30:02 PDT
