Dear Bill,
Thanks for the hint. I got few things from web. Just trying out those.
If I won't succeed then again I will ask in the list.
Thanks again.
On Tue, Feb 12, 2019 at 1:32 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
> Brain slightly more engaged, it seems you are missing a residue
> definition that likely already exists, you just would need to load a
> .lib file for the residue, for example, before loadpdb. Probably an/the
> (?) amber ion tutorial will be enough to help you fill in the blanks, if
> you know your parameters and the relevant literature.
>
> Bill
>
> On 2/11/19 11:37 PM, Bill Ross wrote:
> > Search on the web for calcium residue models (1-atom of course :-) for
> > your C0 residue, which will assign an atom type.
> >
> > 'amber calcium ion' could get you started. You will want to
> > compare/contrast how the ion is handled in different environments, and
> > be able to defend your choices.
> >
> > Bill
> >
> > On 2/11/19 11:22 PM, Sunita Patel wrote:
> >> Dear Amber users,
> >> I am trying to simulate a calcium binding protein with bound calcium.
> >> ff99SB force field am using for that. At the first step itself, am
> getting
> >> following error. Although, I specified the correct atom type for calcium
> >> ions, still it is unable to recognize it.
> >>
> >> Please advise how to counteract the problem. I need the solution
> urgently.
> >>
> >> Please help me. Thanks for the help.
> >>
> >> With best regards,
> >> Sunita
> >>
> >>
> >> ===================
> >> WARNING: The unperturbed charge of the unit: -2.000000 is not zero.
> >> FATAL: Atom .R<Ca 92>.A<C0 1> does not have a type.
> >> FATAL: Atom .R<Ca 93>.A<C0 1> does not have a type.
> >> Failed to generate parameters
> >> Parameter file was not saved.
> >> Quit
> >> ===================
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Received on Tue Feb 12 2019 - 02:30:02 PST
