[gmx-users] how to connect ligating residues?
shumailakhan432 at yahoo.com
Tue Feb 7 06:06:48 CET 2017
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
The specbond.dat file contains the following:
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.
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