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

[Bakary N'tji Diallo]

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

Best regards

-- 

Bakary N’tji DIALLO

PhD Student (Bioinformatics) <http://linkedin.com/in/bakarydiallo>, Research
Unit in Bioinformatics (RUBi) <https://rubi.ru.ac.za/>

Mail: diallobakary4 at gmail.com |  Skype: diallobakary4

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