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

[Mark Abraham]

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