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

[James Starlight]

sorry it was mistake :)

assuming that heme is covalently bonded to the cytochrome by means of 2
cysteines how should I define such bindings (assuming that heme is part of
my protein) based onb the charmm parameters ?
its not clear for me why such connection is absent in the residue.dat
(having HEME included in the rtps)

I still need a example of properly parametrized hem complexed with any
cytochrome :)

James

2013/4/3 James Starlight <jmsstarlight at gmail.com>

> 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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>
>