Assigning Partial Charges to FE in Active Site Superoxide Dismutase.

From: Roy Fernando (roy.nandos_at_gmail.com)
Date: Wed Jan 23 2013 - 13:39:04 CST

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I am trying to use VMD Auto-parametrization tool to create topology and
parameter files for the active site of Superoxide Dismutase (SOD).

The active site contains a FE ion covalently bonded with three nitrogen
atoms of three HIS residues, one oxygen atom from a ASP residue and an
oxygen atom form a solute (water) molecule.

I separated the active side and wrote a pdb file to use as the base
molecule. I am now stuck in the attempt to determine the partial charges to
the active site atoms. Can someone please suggest something for met to hang
on to? IS there a standard set of values I can use and optimize.

Thanks in Advance!

Ajith

• Next message: Gordon Wells: "Re: FEP on an amino acid ligand"
• Previous message: Roy Fernando: "Using CNS parameter file to create NAMD topology and parameter files"
• Next in thread: Norman Geist: "AW: Assigning Partial Charges to FE in Active Site Superoxide Dismutase."
• Reply: Norman Geist: "AW: Assigning Partial Charges to FE in Active Site Superoxide Dismutase."
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