Hello Sir Justin, > Hope so you are doing well. Thanks a lot for your kind response. Thank you very much for your reply.
> Version : 5.0.7 > FF: 43a1 Spc water model. > > Your Suggestion: > "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." > > This oxygen molecule is attached as a ligand to heme. > 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 > > Now my question is how connections to ligating residues should be recognized > via existing entries in specbond.dat. > > 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 > > Waiting for your kind response. I shall be very thankful to you. > > Mehreen Jan -- 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 [email protected].
