Dear Amber users,
I have a biotarget which has magnesium ion together with the small molecule in the binding site. I have made parametrization in GAFF with antechamber for the ligand, but then I've gota problem with magnesium ion. I actually was sure that it is included in the Amber force fields as Na+ ions and I can't find much information in manuals about this. Should I include magnesium ion in the protein or in small ligand or make a separate library for it? Should I use gaff or protein force field?
> saveamberparm rab 1z2ang_w.prmtop 1z2ang_w.inpcrd
Checking Unit.
FATAL: Atom .R<MG 172>.A<MG 1> does not have a type.
Failed to generate parameters
Parameter file was not saved.
Sincerely yours,
Andrew
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Received on Tue Oct 19 2010 - 07:30:04 PDT
