[gmx-users] Problem with FE-Cys covalent bond

[Anthony Cruz Balberdi]

Hi:

Did you add the parameters for the new covalent bond to the correct
part of ffbonded.itp? Because, for the GROMOS FF you have to add the
parameters for the new bond, angle and dihedral ,created due to
specbond, in a certain part of the ffbonded.itp for pdb2gmx be able to
use it. I dont know if the OPLS FF function in the same way but
probably will be something trivial like these. Take a look at the
bottom part of the ffbonded.itp in one of the  GROMOS FF for example
gromos53a5.ff.


Best Regards,

Anthony

On Wed, Jan 11, 2012 at 6:34 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 11/01/2012 7:14 PM, Suman Nandy wrote:
>>
>> Dear gromacs users,
>>
>> I have a problem regarding the simulation of Fe4S4 cluster attached to CYS
>> of a protein using opls ff. I editted the "aminoacids.rtp" file as like
>> this.
>>
>> [ SF4 ]
>> ... [ atoms ]
>> FE1 opls_966 2.500 1
>> FE2 opls_967 2.500 1
>> FE3 opls_968 2.500 1
>> FE4 opls_969 2.500 1
>> S1 opls_970 -2.000 1
>> S2 opls_971 -2.000 1
>> S3 opls_972 -2.000 1
>> S4 opls_973 -2.000 1
>> [ bonds ]
>> FE1 S1
>> FE1 S2
>> FE1 S3
>> FE2 S1
>> FE2 S2
>> FE2 S4
>> FE3 S2
>> FE3 S3
>> FE3 S4
>> FE4 S1
>> FE4 S2
>> FE4 S3
>>
>> and also "atomtypes.atp" as
>>
>> opls_966 55.84500 ; FE1: HEME
>> opls_967 55.84500 ; FE2: HEME
>> opls_968 55.84500 ; FE3: HEME
>> opls_969 55.84500 ; FE4: HEME
>> opls_970 32.06000 ; S1: S
>> opls_971 32.06000 ; S2: S
>> opls_972 32.06000 ; S3: S
>> opls_973 32.06000 ; S4: S
>>
>> I have also added a line to "specbond.dat" regarding the SG-FE covalent
>> bond. But while running the pdb2gmx command, (withouit any error) it just
>> adds a H with SG (where the FE to bind)and there is no information on SG-FE
>> bond in topology file. Please help.
>
>
> You should inspect the output of pdb2gmx to see what it thinks about the
> sulfur cluster.  It's either not close enough or not considered part of the
> same [moleculetype] being created. You may need to choose PDB chain IDs and
> pdb2gmx -chainsep more suitably.
>
> Mark
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