From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Jan 24 2013 - 01:23:18 CST
The partial charges are usually determined by a QM simulation when building
new residues. You could be interested in RESP ESP Charge derive Server,
which uses Gamess for it. Don't know if this is suitable for charm.
Norman Geist.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Roy Fernando
Gesendet: Mittwoch, 23. Januar 2013 20:39
An: namd-l_at_ks.uiuc.edu; vmd-l_at_ks.uiuc.edu
Betreff: namd-l: Assigning Partial Charges to FE in Active Site Superoxide
Dismutase.
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
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