[gmx-users] Simulation of the HEM-containing proteins
James Starlight
jmsstarlight at gmail.com
Fri Apr 12 20:28:01 CEST 2013
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 <jmsstarlight at gmail.com>
> 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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>>
>>
>
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