[gmx-users] Simulation of the HEM-containing proteins

[Justin Lemkul]

On Wed, Apr 3, 2013 at 8:24 AM, James Starlight <jmsstarlight at gmail.com>wrote:

> Dear Gromacs users!
>
>
> I want to simulate Cytochrome C in complex with HEM using NMR full-atom
> structure of that protein as the starting conformation and charm36 force
> field's parameters.
>
> in the charm36 ff I've found parameters for HEM but I have not found params
> for the hydrogens (in the aminoacids.hdb file) as well as definition of the
> HEM as the part of the protein in the residuetypes.dat ( including
> connection to the rest of polypeptide chain ).
>
> So during pdb2gmx parametrisation I've obtained errors like
>
> WARNING: atom HA is missing in residue HEME 105 in the pdb file
>          You might need to add atom HA to the hydrogen database of building
> block HEME
>          in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HB is missing in residue HEME 105 in the pdb file
>          You might need to add atom HB to the hydrogen database of building
> block HEME
>          in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HC is missing in residue HEME 105 in the pdb file
>          You might need to add atom HC to the hydrogen database of building
> block HEME
>          in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HD is missing in residue HEME 105 in the pdb file
>          You might need to add atom HD to the hydrogen database of building
> block HEME
>          in the file aminoacids.hdb (see the manual)
>
>
> Have anybody such missing parameters?
>
>
There aren't missing parameters, per se.  The parameters are all there in
the .rtp and other force field files.  You just need to construct an .hdb
entry for HEM, as pdb2gmx says.  See the manual, section 5.6.4.

-Justin

-- 

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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