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
> /
> _______________________________________________
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> 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
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Received on Wed Feb 15 2012 - 07:30:03 PST
