Hi Help,
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.
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.
Your help is appreciated about how to get sleap work with amoeba potentials?
I tried the test/sleap examples and it runs. I also tried the above example
of chloride ion in water and it works.
Regards,
Neha
On 16 September 2011 03:08, David A Case <case.biomaps.rutgers.edu> wrote:
> On Thu, Sep 15, 2011, Neha Gandhi wrote:
> >
> > AMBER includes AMOEBA potentials but what water potentials are suitable
> > along with it? Can i use flexible water model in AMBER11?
>
> The expectation is that you will use the AMOEBA water potential if you have
> an
> AMOEBA solute. I'm not sure whether or not other combinations will work,
> either in the sense of giving the expected energies, or in the sense of
> giving
> a good account of reality.
>
> ...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 Tue Oct 04 2011 - 03:00:02 PDT
