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

Thu Apr 11 14:12:25 CEST 2013

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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>
>