Re: VdW parameters for Zn and Fe in metalloproteins

From: felmerino_at_uchile.cl
Date: Sat Nov 13 2010 - 18:10:23 CST

Hey,

Ther service mentioned by Flavio is based on the Merk Molecular Force Field. Mixing these parameters with those of CHARMM seems to be not a very good idea. It was briefly discussed in the CHARMM forum as well (http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=24441).

best

Felipe

----Mensaje original----

De: oivalf_nix_at_yahoo.com

Fecha: 13-11-2010 17:06

Para: "NAMD Users' List"<namd-l_at_ks.uiuc.edu>, "Erik Nordgren"<nordgren_at_sas.upenn.edu>

Asunto: Re: namd-l: VdW parameters for Zn and Fe in metalloproteins

Hi Eric,

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
GROMACS.

Good Luck,

Flavio

--- 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

Hi folks,

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

    FE 0.010000 0.000000 0.650000 ! ALLOW HEM
                    ! 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?

thanks,
Erik

-- 
C. Erik Nordgren, Ph.D.
Chemistry Department
University of Pennsylvania

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