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

James Starlight jmsstarlight at gmail.com
Fri Apr 12 11:04:55 CEST 2013 

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 separate itp file in the topology) should'n it ?
How I can define coordinate bond of the heme's FE atom with the cysteine
side chain (in the pdb2gmx I found that such can be done only for
histidines)?

James

2013/4/12 Mark Abraham <mark.j.abraham at gmail.com>

> Look in the literature...
>
>
> On Thu, Apr 11, 2013 at 2:12 PM, James Starlight <jmsstarlight at gmail.com
> >wrote:
>
> > 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) for any ful-atomic force field? Finally I've not found in mailing
> > list any possible sollution of the same problems.
> >
> >
> > James
> >
> > 2013/4/4 James Starlight <jmsstarlight at gmail.com>
> >
> > > 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 residuetype.dat as the part of the
> > > protein?
> > >
> > > Finally I'll be thankful to everyone who could provide me with the any
> > > cytochrome properly parametrized in charmm :)
> > >
> > > James
> > >
> > >
> > > 2013/4/3 Justin Lemkul <jalemkul at vt.edu>
> > >
> > >> On Wed, Apr 3, 2013 at 10:27 AM, James Starlight <
> > jmsstarlight at gmail.com
> > >> >wrote:
> > >>
> > >> > 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, line 3153]:
> > >> >   No default Bond types
> > >> >
> > >> >
> > >> > ERROR 4 [file topol.top, line 8725]:
> > >> >   No default U-B types
> > >> >
> > >> >
> > >> > ERROR 5 [file topol.top, line 8792]:
> > >> >   No default U-B types
> > >> >
> > >> >
> > >> > ERROR 6 [file topol.top, line 10624]:
> > >> >   No default U-B types
> > >> >
> > >> >
> > >> > ERROR 7 [file topol.top, line 10625]:
> > >> >   No default U-B types
> > >> >
> > >> >
> > >> > ERROR 8 [file topol.top, line 11382]:
> > >> >   No default U-B types
> > >> >
> > >> >
> > >> > ERROR 9 [file topol.top, line 11383]:
> > >> >   No default U-B types
> > >> >
> > >> >
> > >> > ERROR 10 [file topol.top, line 11384]:
> > >> >   No default U-B types
> > >> >
> > >> >
> > >> > ERROR 11 [file topol.top, line 11385]:
> > >> >   No default U-B types
> > >> >
> > >> >
> > >> > ERROR 12 [file topol.top, line 11491]:
> > >> >   No default U-B types
> > >> >
> > >> >
> > >> > ERROR 13 [file topol.top, line 11492]:
> > >> >   No default U-B types
> > >> >
> > >> >
> > >> > ERROR 14 [file topol.top, line 11493]:
> > >> >   No default U-B types
> > >> >
> > >> >
> > >> > ERROR 15 [file topol.top, line 11506]:
> > >> >   No default U-B types
> > >> >
> > >> >
> > >> > ERROR 16 [file topol.top, line 11507]:
> > >> >   No default U-B types
> > >> >
> > >> >
> > >> > ERROR 17 [file topol.top, line 11508]:
> > >> >   No default U-B types
> > >> >
> > >> >
> > >> > ERROR 18 [file topol.top, line 12147]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 19 [file topol.top, line 12148]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 20 [file topol.top, line 12149]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 21 [file topol.top, line 12150]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 22 [file topol.top, line 12151]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 23 [file topol.top, line 12152]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 24 [file topol.top, line 12247]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 25 [file topol.top, line 12248]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 26 [file topol.top, line 12249]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 27 [file topol.top, line 12250]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 28 [file topol.top, line 12251]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 29 [file topol.top, line 12252]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 30 [file topol.top, line 14948]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 31 [file topol.top, line 14950]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 32 [file topol.top, line 14952]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 33 [file topol.top, line 14956]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 34 [file topol.top, line 14957]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 35 [file topol.top, line 14958]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 36 [file topol.top, line 14959]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 37 [file topol.top, line 14960]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 38 [file topol.top, line 14961]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 39 [file topol.top, line 14962]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 40 [file topol.top, line 14963]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 41 [file topol.top, line 14964]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 42 [file topol.top, line 14965]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 43 [file topol.top, line 14966]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 44 [file topol.top, line 16263]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 45 [file topol.top, line 16264]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 46 [file topol.top, line 16269]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> >
> > >> > ERROR 47 [file topol.top, line 16270]:
> > >> >   No default Proper Dih. types
> > >> >
> > >> > Excluding 3 bonded neighbours molecule type 'Protein'
> > >> > Excluding 2 bonded neighbours molecule type 'SOL'
> > >> >
> > >> > NOTE 3 [file topol.top, line 16745]:
> > >> >   System has non-zero total charge: 7.000001
> > >> >   Total charge should normally be an integer. See
> > >> >   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> > >> >   for discussion on how close it should be to an integer.
> > >> >
> > >> >
> > >> > -------------------------------------------------------
> > >> > Program grompp, VERSION 4.6
> > >> > Source code file:
> > >> > /home/own/Documents/distr/gromacs-4.6/src/kernel/grompp.c, line:
> 1593
> > >> >
> > >> > Fatal error:
> > >> > There were 47 errors in input file(s)
> > >> > For more information and tips for troubleshooting, please check the
> > >> GROMACS
> > >> > website at http://www.gromacs.org/Documentation/Errors
> > >> >
> > >> > During visualization of the complex.gro file I didnt observe any
> > >> > distortions in the geometry of heme-cytochrome complex (it looks
> like
> > >> NMR
> > >> > structure) but why that errors occured ?
> > >> >
> > >> >
> > >> Heme is tricky, and this error comes up every time someone tries to
> use
> > >> heme in Gromacs (see the archive for tips and possible solutions).
> > >>  Parameters are missing for bonded interactions, so either add them
> > >> directly to the .top or to ffbonded.itp.  You'll have to search the
> > >> literature for suitable parameters or derive them yourself.  There are
> > >> lots
> > >> of reports of heme-containing proteins being simulated, so clearly the
> > >> fully parameter set exists somewhere.
> > >>
> > >> -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
> > >>
> > >> ========================================
> > >> --
> > >> gmx-users mailing list    gmx-users at gromacs.org
> > >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> > >> * Please search the archive at
> > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > >> * Please don't post (un)subscribe requests to the list. Use the
> > >> www interface or send it to gmx-users-request at gromacs.org.
> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>
> > >
> > >
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>

More information about the gromacs.org_gmx-users mailing list