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 - 06:30:04 PDT
