Hello Sir, Hopefully you are doing well. As I am new to GROMACS, I am facing problems. I read your comments and You suggested someone that "You should not need external servers to generate a heme topology; GROMOS already supports it. It's called HEME and it's in the .rtp file. Connections to ligating residues should be recognized via existing entries in specbond.dat." I am using Version : 5.0.7 Force Feild : 43a1 Spc water model. The ligand attached to heme is oxygen molecule. HETATM 1 O1 OXY C1543 5.525 80.353 -6.212 1.00 25.38 O HETATM 2 O2 OXY C1543 4.301 80.342 -6.721 1.00 30.35 O END
The specbond.dat file contains the following: 8 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 Kindly please guide me, how connections to ligating residues should be recognized via existing entries in specbond.dat? I shall be very thankful to you. Shumaila khan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
