[gmx-users] How to connect ligating residues ??

[Mehreen Jan]

Hello,
         Hope so you are doing well. Thanks a lot for your kind response.
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