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

[James Starlight]

hmm

I've done parametrization of the hem using standart charmm36 parameters but
indeed there is some confusing with the hydrogens

for example my pdb (obtained from NMR structure) consist of 2 extra
hydrogens (which both parts of the methyl groups) which are not present in
the rtp parameters. So if I delete both of that hydrogens from pdb- my HEM
will be -2 charged. On tyhe other hands hem in my pdb lack of 2 protons in
the COOH groups. Could someone provide me with the HEM (in planargeometry)
parametrized in charmm36 ?

By the way assuming that the HEM itself is not covalently bonded to the
rest of the protein ( as in the case of GFP or rhodopsin). So the
parameters for the hem should be included as the any other diffusiable
ligand (as the separate itp file) in topology, should'n it?

James


2013/4/3 Justin Lemkul <jalemkul at vt.edu>

> 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
>
> --
>
> ========================================
>
> 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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