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.
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