Dear all,
I'm currently trying to simulate a Cytochrome P450 protein in solution and am
having trouble getting the system to give a cysteine molecule correct partial
charges in Gromacs 2018.1. In my system the CYS400 residue should ligate to the
HEM(471) motif and, from the PDB file, I have measured a distance of 2.45A.
Furthermore, given the oxidation states of the heme and CYS residues, I have
assigned their charges from previous work and labelled these states as HEME and
CYS2 in the aminoacids.rtp & aminoacids.hdb files.
My Specbond.dat file is as follows:
8
CYS SG 1 CYS SG 1 0.2 CYS2 CYS2
CYS SG 2 HEM FE 1 0.245 CYS2 HEME
CYS SG 1 HEM CAB 1 0.18 CYS2 HEME
CYS SG 1 HEM CAC 1 0.18 CYS2 HEME
HIS NE2 1 HEM FE 1 0.2 HIS1 HEME
MET SD 1 HEM FE 1 0.24 MET HEME
CO C 1 HEME FE 1 0.19 CO HEME
CYM SG 1 CYM SG 1 0.2 CYS2 CYS2
The output of Special Atom Distance Matrix is as follows (from pdb2gmx):
MET354 HIS361 HIS388 CYS400 HIS408 MET416 MET417
SD2900 NE22958 NE23198 SG3288 NE23352 SD3407 SD3415
HIS361 NE22958 1.532
HIS388 NE23198 1.727 1.150
CYS400 SG3288 1.774 1.327 1.535
HIS408 NE23352 3.256 2.299 2.642 1.541
MET416 SD3407 3.668 2.718 3.359 2.161 0.974
MET417 SD3415 3.175 2.259 3.133 2.007 1.445 0.859
HIS420 NE23443 4.155 3.126 3.848 2.737 1.531 0.624 1.064
HIS426 NE23500 3.635 2.987 4.077 3.111 2.916 2.214 1.473
HEM471 CAB3759 1.871 1.235 1.869 0.607 1.452 1.810 1.477
HEM471 CAC3760 2.127 1.870 2.107 0.595 1.426 1.965 1.925
HEM471 FE3800 1.627 1.359 1.644 0.245 1.692 2.229 2.013
However, whenever I run pdb2gmx, I find that CYS400 has been assigned as a CYS
resiude, and not CYS2, leading to non-integer charge (the CYS2 parameters
should yield integer charge). If anyone has any thoughts on where I'm going
wrong, I would be eternally grateful.
Many thanks,
Matthew
Matthew Fisher
DPhil Candidate in Inorganic Chemistry (L.L.Wong Group)
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