Dear AMBER users,
I have protein in which Magnesium ion is forming octahedral coordination
geometry with the atoms of active site viz. 3 point interactions with the
ligand oxygens, 2 interactions with conserved water molecules and 1
interaction with side chain oxygen of Asn amino acid. My main concern is
about the effective charge on the Magnesium ion. I read literature where
they have used charge on Mg as 0.9 instead of +2, due to distribution of
electrons between the interacting atoms.
While preparing the input files inpcrd and prmtop for protein in AMBER, I
found that total effective charge on protein is 5.9 (including charge 0.9 of
Mg). So accordingly I added 5 Cl- ions to it. But, keep the total charge as
+0.9 (Mg). Is it a correct way to perform dynamics or otherwise I have to
add 1 more Cl- ion to make the effective charge as -0.1.
Please help me in this regard.
Thanks a lot.
--
*Warm Regards *
Vaibhav Jain
Ph.D. Scholar
Centre For Pharmacoinformatics
NIPER, Mohali (Punjab)
MOb no. +919988412195
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Received on Fri Apr 15 2011 - 07:30:02 PDT
