[gmx-users] specbond .dat fie : any one plz modify it......tell me how to modify it..

[Mehreen Jan]

Hello, anyone plz help
               Hopefully you all are doing well.
I am using FF: 43a1
  Spc watermodel
version 5.0.7.

I know parameters for Heme are already available and that is for FE2+. I want to perform MD simulation for FE3+. While running simulation I get error : Residue "OXY" not found in residue topology database. I checked .rtp file and that does not include topology for OXY. I checked gromacs mailing list and got the answer that modify specbond . dat file . Kindly please brief me how should I modify specbond .dat file so that I could include oxygen molecule.  i read manual  5.6.7 Special bonds but i am still not able to connect OXY with HEME.  This is my oxygen

HETATM 2414  O1  OXY C1543       5.525  80.353  -6.212  1.00 25.38           O
HETATM 2415  O2  OXY C1543       4.301  80.342  -6.721  1.00 30.35           O 

  specbond .dat fie : any one plz modify it......

9
CYS    SG    1    CYS    SG    1    0.2    CYS2    CYS2
CYS    SG    1    HEM     FE    2    0.25    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
CYZ     SG      1       ZN1     ZN      1       0.23    CYZ     ZN1
                                                                               
                                                                             Thanks,
                                                                                           Mehreen Jan