[gmx-users] About ligands and metals in specbond.dat

[Justin Lemkul]

On 7/3/19 3:49 AM, Bakary N'tji Diallo wrote:
> Hello
> I am adding parameters  for a manganese atom in a force field in Gromacs
> following the guide here:
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
> I have a question about step 6: "If the residue involves special
> connectivity to other residues, update specbond.dat."
> For the coordinating residues GLU and ASP there is no problem. The
> manganese atom is also connected to a ligand in the protein for which I may
> know the ID (here LC5)
> but the ligand may vary in which case it may be difficult to predict the
> ID. It is possible to use
> a 'wildcard' approach to account for that? I tried XXX without success.
> So far my specbond.dat looks like bellow:
>    1 17
>    2 CYS     SG      1       CYS     SG      1       0.2     CYS2    CYS2
>    3 CYS     SG      1       HEM     FE      2       0.25    CYS2    HEME
>    4 CYS     SG      1       HEM     CAB     1       0.18    CYS2    HEME
>    5 CYS     SG      1       HEM     CAC     1       0.18    CYS2    HEME
>    6 HIS     NE2     1       HEM     FE      1       0.2     HIS1    HEME
>    7 MET     SD      1       HEM     FE      1       0.24    MET     HEME
>    8 CO      C       1       HEME    FE      1       0.19    CO      HEME
>    9 CYM     SG      1       CYM     SG      1       0.2     CYS2    CYS2
>   10 MN      MN      6       ASP     OD1     1       0.21    MN      ASP
>   11 MN      MN      6       ASP     OD2     1       0.21    MN      ASP
>   12 MN      MN      6       GLU     OE1     1       0.21    MN      GLU
>   13 MN      MN      6       GLU     OE2     1       0.21    MN      GLU
>   14 MN      MN      6       LC5     O       1       0.21    MN      LC5
>   15 MN      MN      6       XXX     O       1       0.21    MN      XXX
>   16 MN      MN      6       LC5     O2      1       0.21    MN      LC5
>   17 MN      MN      6       XXX     O2      1       0.21    MN      XXX

The specbond.dat file requires real residue names. As you have it, 
pdb2gmx is going to try to match XXX.

-Justin

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Justin A. Lemkul, Ph.D.
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