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

[Mark Abraham]

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