[gmx-users] How to connect ligating residues ??
mehreen_jan1990 at yahoo.com
Tue Feb 7 07:06:10 CET 2017
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
> 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:
> 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
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