Your best bet might be to make a modified amino acid residue that has the
calcium bound to it. I think there is an AMBER tutorial on exactly that
issue, some histidines bound to a zinc or something of the sort, should be
easy to look up.
On Wed, Feb 15, 2012 at 10:22 AM, Brian Radak <radak004.umn.edu> wrote:
> Hi Quentin,
>
> As you found, this is a common question on the mailing list. You should be
> aware that divalent cations are still a significant problem for fixed
> charge force fields. I don't believe there is any commonly accepted
> parameterization for calcium, especially amongst the AMBER community. I
> would be careful with what Leap gives you (even when you do get it to
> "work").
>
> Regards,
> Brian
>
> On Wed, Feb 15, 2012 at 10:02 AM, Quentin Delettre <delettre.ipmc.cnrs.fr
> >wrote:
>
> > Dear Amber users,
> >
> > I'm new on amber and trying to do start a MD simulation of my protein
> > with one calcium ion binded by a loop, in explicit solvent.
> >
> > In my PDB file, i have at the end
> >
> > TER 1038 ASN 130
> > ATOM 1039 KA CAL 131 38.176 33.816 20.115 1.00
> > 15.29 C0
> > END
> >
> > I have searched on the board and found theses answers :
> >
> > http://archive.ambermd.org/201102/0357.html
> >
> > http://archive.ambermd.org/200709/0211.html
> >
> > http://archive.ambermd.org/200807/0389.html
> >
> > but infortunately, whatever i try with these explanations :
> >
> > (Residue 130: CAL, Terminal/last, was not found in name map.)
> >
> > Meaning that my residue and atom type is not found.
> >
> >
> > Can you give me examples or tutorials of amber simulation with ions ?
> >
> > /Best regards,
> >
> > Quentin Delettre
> > /
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Center for Integrative
> Proteomics Room 308
> Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> Department of Chemistry : Piscataway, NJ
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> radakb.biomaps.rutgers.edu
> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute appropriate
> address.
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--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Wed Feb 15 2012 - 08:00:02 PST
