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.
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
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!
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