by the way also I've tried to make model of cytochrome p450 in charmm. In
that case heme have only one coordinate bond with the side chain of
cysteine (not 2 covalent bonds with cysteines as in the cytochrome-C). So
as I understand I should include model of heme as the diffusion ligand ( as
the
I forgot to point out that when I made topology for cytochrome-HEME complex
( assuming one cysteine covalently bonded to the FE ) again I've forced
with the lack of charmm parameters for such cysteine-HEME interactions (
I've only found it for His coordinating bond).
ERROR 1 [file topol.top, line
also I found such parameters in the native charm format (.prm)
could you provide me with some script for conversion of tpr to itp? I could
do such topology for cytochrome and add it to the contribution :)
James
2013/4/12 James Starlight jmsstarli...@gmail.com
I forgot to point out that when I
During the past few days I've tried to make parametrization of any
heme-containing cythochromes and always failed with the huge errors about
missing parameters. Could someone provide me with such params (i suppose it
should be added to thebonded/non-bonded.itps of the force field besides the
rtps)
Look in the literature...
On Thu, Apr 11, 2013 at 2:12 PM, James Starlight jmsstarli...@gmail.comwrote:
During the past few days I've tried to make parametrization of any
heme-containing cythochromes and always failed with the huge errors about
missing parameters. Could someone provide me
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
On Wed, Apr 3, 2013 at 8:24 AM, James Starlight jmsstarli...@gmail.comwrote:
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
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
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
I've successfully parametrize cytochrome-HEME complex by means pdb2gmx but
after processing that structure to grompp I've obtained errors like
ERROR 1 [file topol.top, line 2106]:
No default Bond types
ERROR 2 [file topol.top, line 2144]:
No default Bond types
ERROR 3 [file topol.top,
On Wed, Apr 3, 2013 at 10:27 AM, James Starlight jmsstarli...@gmail.comwrote:
I've successfully parametrize cytochrome-HEME complex by means pdb2gmx but
after processing that structure to grompp I've obtained errors like
ERROR 1 [file topol.top, line 2106]:
No default Bond types
ERROR 2
It was strange for me the big number of such errors :)
May the construction of new scheme for the hydrogens in the .hdb file
partly solve my problem ? ( as I've mentioned previously i had mismatch in
2 hydrogens ( in comparison to the NMR-like structure).
Should also HEME be added in the
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