You need to rename the atom to match what AMBER is expecting. I'm not sure
what it is expecting, but almost certainly the atom and residue should be
the same, for instance sodium would be:
ATOM 1039 NA+ NA+ 131 .........
you can open leap and try things like "edit CA+" and see if that is
something that already exists. Unless someone else already knows what the
name should be.
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
> /
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Wed Feb 15 2012 - 07:30:02 PST
