I don't know which GB model you are using, but I expect that they will not
work well for many ions, especially ones that are not monovalent. I'm not
sure I understand the rest of your email about "bond between ligands were
defined".
On Fri, Apr 8, 2016 at 9:13 AM, Vasantha Kumar <vin.vasanth.gmail.com>
wrote:
> Dear AMEBR users
>
> Is it possible to obtain proper tetrahedral metal geometry for a modified
> peptide, whose structure was calculated using nmr restraints and using
> AMBER in restrained MD method.
> I am currently using non-boded ZAFF model to handle zinc. In my calculation
> of 200ps rMD in GB model metal geometry is deviated from ideal geometry
> (tetrahedral to trigonal bipyramidal). For the moment I have removed the
> nmr restraints in the coordination, because on the ligand peaks was not
> identified due to sever overlap and since bond between ligands were
> defined. Could any one suggest me in solution NMR structure is it possible
> to maintain geometry in rMD protocol.
>
> thanks in advance
> Vince
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Received on Fri Apr 08 2016 - 08:00:03 PDT
