[gmx-users] Simulation of the HEM-containing proteins
James Starlight
jmsstarlight at gmail.com
Fri Apr 12 13:50:50 CEST 2013
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 12409]:
No default Bond types
ERROR 2 [file topol.top, line 40454]:
No default U-B types
ERROR 3 [file topol.top, line 42130]:
No default U-B types
ERROR 4 [file topol.top, line 42131]:
No default U-B types
ERROR 5 [file topol.top, line 42132]:
No default U-B types
ERROR 6 [file topol.top, line 42133]:
No default U-B types
ERROR 7 [file topol.top, line 56994]:
No default Proper Dih. types
ERROR 8 [file topol.top, line 56995]:
No default Proper Dih. types
ERROR 9 [file topol.top, line 56996]:
No default Proper Dih. types
ERROR 10 [file topol.top, line 56997]:
No default Proper Dih. types
ERROR 11 [file topol.top, line 56998]:
No default Proper Dih. types
ERROR 12 [file topol.top, line 56999]:
No default Proper Dih. types
ERROR 13 [file topol.top, line 57000]:
No default Proper Dih. types
Also I've looked the literature for such parameters suitable for charm but
didnt find anything.
Does anybody here tried to simulate cytochrome ?
James
2013/4/12 James Starlight <jmsstarlight at gmail.com>
> 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
>> > >>
>> > >> ========================================
>> > >> --
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>> > >
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