[gmx-users] Issues with specbond.dat for a HEME protein

[Matthew Fisher]

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)