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

[James Starlight]

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 ?


James

2013/4/3 James Starlight <jmsstarlight at gmail.com>

> sorry it was mistake :)
>
> assuming that heme is covalently bonded to the cytochrome by means of 2
> cysteines how should I define such bindings (assuming that heme is part of
> my protein) based onb the charmm parameters ?
> its not clear for me why such connection is absent in the residue.dat
> (having HEME included in the rtps)
>
> I still need a example of properly parametrized hem complexed with any
> cytochrome :)
>
> James
>
>
> 2013/4/3 James Starlight <jmsstarlight at gmail.com>
>
>> hmm
>>
>> I've done parametrization of the hem using standart charmm36 parameters
>> but indeed there is some confusing with the hydrogens
>>
>> for example my pdb (obtained from NMR structure) consist of 2 extra
>> hydrogens (which both parts of the methyl groups) which are not present in
>> the rtp parameters. So if I delete both of that hydrogens from pdb- my HEM
>> will be -2 charged. On tyhe other hands hem in my pdb lack of 2 protons in
>> the COOH groups. Could someone provide me with the HEM (in planargeometry)
>> parametrized in charmm36 ?
>>
>> By the way assuming that the HEM itself is not covalently bonded to the
>> rest of the protein ( as in the case of GFP or rhodopsin). So the
>> parameters for the hem should be included as the any other diffusiable
>> ligand (as the separate itp file) in topology, should'n it?
>>
>> James
>>
>>
>>
>> 2013/4/3 Justin Lemkul <jalemkul at vt.edu>
>>
>>> On Wed, Apr 3, 2013 at 8:24 AM, James Starlight <jmsstarlight at gmail.com
>>> >wrote:
>>>
>>> > Dear Gromacs users!
>>> >
>>> >
>>> > I want to simulate Cytochrome C in complex with HEM using NMR full-atom
>>> > structure of that protein as the starting conformation and charm36
>>> force
>>> > field's parameters.
>>> >
>>> > in the charm36 ff I've found parameters for HEM but I have not found
>>> params
>>> > for the hydrogens (in the aminoacids.hdb file) as well as definition
>>> of the
>>> > HEM as the part of the protein in the residuetypes.dat ( including
>>> > connection to the rest of polypeptide chain ).
>>> >
>>> > So during pdb2gmx parametrisation I've obtained errors like
>>> >
>>> > WARNING: atom HA is missing in residue HEME 105 in the pdb file
>>> >          You might need to add atom HA to the hydrogen database of
>>> building
>>> > block HEME
>>> >          in the file aminoacids.hdb (see the manual)
>>> >
>>> >
>>> > WARNING: atom HB is missing in residue HEME 105 in the pdb file
>>> >          You might need to add atom HB to the hydrogen database of
>>> building
>>> > block HEME
>>> >          in the file aminoacids.hdb (see the manual)
>>> >
>>> >
>>> > WARNING: atom HC is missing in residue HEME 105 in the pdb file
>>> >          You might need to add atom HC to the hydrogen database of
>>> building
>>> > block HEME
>>> >          in the file aminoacids.hdb (see the manual)
>>> >
>>> >
>>> > WARNING: atom HD is missing in residue HEME 105 in the pdb file
>>> >          You might need to add atom HD to the hydrogen database of
>>> building
>>> > block HEME
>>> >          in the file aminoacids.hdb (see the manual)
>>> >
>>> >
>>> > Have anybody such missing parameters?
>>> >
>>> >
>>> There aren't missing parameters, per se.  The parameters are all there in
>>> the .rtp and other force field files.  You just need to construct an .hdb
>>> entry for HEM, as pdb2gmx says.  See the manual, section 5.6.4.
>>>
>>> -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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>>
>>
>