[gmx-users] protein-ligand interactions in charmm force field

[James Starlight]

Dear Gromacs users!

At present time I'm simulating protein-ligand complexes parametrized
in Charmm force field. In particular I'm not quite sure aboout
correctness of params made for my ligands by SwissParams. So I wounder
to know the suggestions from the people which already prepared their
systems including ligands parametrized by swiss-param (About possible
corrections in that topologies)

for example this is the topology of small drug-like mollecule
isoprenaline which I simulate with membrane receptor

[ atoms ]
; nr type resnr resid atom cgnr charge mass
   1 CB   1  LIG C9      1  0.0825  12.0110
   2 CB   1  LIG C11     2  0.0825  12.0110
   3 CB   1  LIG C10     3 -0.1500  12.0110
   4 CB   1  LIG C7      4 -0.1500  12.0110
   5 CB   1  LIG C4      5 -0.1435  12.0110
   6 CB   1  LIG C8      6 -0.1500  12.0110
   7 CR   1  LIG C5      7  0.0000  12.0110
   8 CR   1  LIG C2      8  0.5030  12.0110
   9 NRP  1  LIG N1      9 -0.9060  14.0067
  10 HNRP 1  LIG H4     10  0.4500   1.0079
  11 HNRP 1  LIG H5     11  0.4500   1.0079
  12 CR   1  LIG C3     12  0.5030  12.0110
  13 OR   1  LIG O3     13 -0.5325  15.9994
  14 HOCC 1  LIG H3     14  0.4500   1.0079
  15 OR   1  LIG O2     15 -0.5325  15.9994
  16 HOCC 1  LIG H2     16  0.4500   1.0079
  17 HCMM 1  LIG H18    17  0.1500   1.0079
  18 HCMM 1  LIG H16    18  0.1500   1.0079
  19 CR   1  LIG C1     19  0.4235  12.0110
  20 OR   1  LIG O1     20 -0.6800  15.9994
  21 HOR  1  LIG H1     21  0.4000   1.0079
  22 HCMM 1  LIG H17    22  0.1500   1.0079
  23 CR   1  LIG C6     23  0.0000  12.0110
  24 HCMM 1  LIG HC2    24  0.0000   1.0079
  25 HCMM 1  LIG HC3    25  0.0000   1.0079
  26 HCMM 1  LIG HC     26  0.0000   1.0079
  27 HCMM 1  LIG HC1    27  0.0000   1.0079
  28 HCMM 1  LIG HC4    28  0.0000   1.0079
  29 HCMM 1  LIG HC5    29  0.0000   1.0079
  30 HCMM 1  LIG HC6    30  0.0000   1.0079
  31 HCMM 1  LIG HC7    31  0.0000   1.0079
  32 HCMM 1  LIG HC8    32  0.0000   1.0079
  33 HCMM 1  LIG HC9    33  0.0000   1.0079

from that atom set two polar OH groups are crusial for establishment
of the polar interaction with some side-chains of my proteins within
its ligand-binding pocket.

  13 OR   1  LIG O3     13 -0.5325  15.9994
  14 HOCC 1  LIG H3     14  0.4500   1.0079
  15 OR   1  LIG O2     15 -0.5325  15.9994
  16 HOCC 1  LIG H2     16  0.4500   1.0079

Im not sure about correctness of charge distribution of that residues
but in fact of my md trajectory I've observed only very rarely h-bond
establishment between that OH and some Ser residues (which are seen in
the X-ray structures of that protein).

By the way does it possible to obtain some XVG graphs for H_bond
distances (using g_hbond tool) between separate ligand functional
groups and protein polar side chains (in a manner of graphs which are
produced by g_saltbr )?

Thanks for help,

James