[gmx-users] How should I modify specbond . dat file?

[Shumaila Khan]

Hello,               Hopefully you all are doing well.I am using FF: 43a1 and Spc watermodel and 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. Kindly find the attachment . I have attached the complete structure. Kindly Please help me out.                                                                                                                                                              Thanks,                                                                                           Shumaila Khan