[gmx-users] Recognizing the Fe-S bond in Hemprotein by pdb2gmx

[zeineb SI CHAIB]

Dear gmx users, 

I'm working on a Hemprotein (homodimer) and I'm having some troubles with pdb2gmx in order to recognize the Fe-S bond (between the hem and a residue of my protein): 

In my pdb2gmx command, I'm using chainsep option in a way that the HEM and the protein belongs to the same chain. For the first monomer the distance between Fe - S = 0.223 nm and in the second one it is Fe - S = 0.229 nm

The weird thing is that pdb2gmx only recognise the bond in the second monomer (according to its input: Linking CYS-410 SG-474 and HEM-698 FE-2774 when treating the second monomer and nothing for the first one)!

But when I change the distance in specbond.dat: 

CYS    SG    1    HEM     FE    2    0.23    CYS2    HEME      (0.23 instead of 0.25) with one copy of specbond in CHARMM27.ff (of my working directory) and another copy in the same general forlder where there is the rest of the input files, pdb2gmx recognise the bond in the 2 monomers!!? 

Is there another way to do that without having multiple copies of the same file everywhere or just in the CHARMM ff folder?! 

Best regards. 

Zeineb.