From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Sat Nov 13 2010 - 14:06:59 CST
Have you ever tried Swiss Param at http://swissparam.ch/
This service provides topology and parameters for small organic molecules
compatible with the CHARMM all atoms force field, for use with CHARMM and
--- On Sat, 11/13/10, Erik Nordgren <nordgren_at_sas.upenn.edu> wrote:
From: Erik Nordgren <nordgren_at_sas.upenn.edu>
Subject: namd-l: VdW parameters for Zn and Fe in metalloproteins
To: "NAMD Users' List" <namd-l_at_ks.uiuc.edu>
Date: Saturday, November 13, 2010, 4:05 AM
I'm wondering if anyone knows of a reference where I could obtain nonbonded parameters (compatible with the CHARMM force field) appropriate for Zn(II) in a Zn-porphyrin cofactor within a metalloprotein? I've spent a good amount of time searching but haven't managed to find what I need... but hopefully I've just been looking in the wrong places!
Now, the standard CHARMM22 protein parameters (e.g., "par_all27_prot_lipid.prm") do include these two lines:
ZN 0.000000 -0.250000 1.090000 ! ALLOW ION
! RHS March 18, 1990
! Heme (6-liganded): Iron atom (KK 05/13/91)
.. but I'm pretty sure that Zn entry is specifically for an isolated Zn(+2) ion, which would have rather different parametrization from that of a covalently-coordinated Zn atom.
Also, while I'm at it, another question: does anyone know why the parameter entry here for heme-iron is different from every other nonbonded term in the FF, in the sense that the first number (supposedly ignored) is non-zero, and the second number (epsilon, the potential well depth) is zero? Doesn't this mean that Fe atoms using this parameter would not have any VdW interaction with other atoms whatsoever?
-- C. Erik Nordgren, Ph.D. Chemistry Department University of Pennsylvania
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