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

[Mehreen Jan]

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