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

[James Starlight]

by the way could someone provide me with some simple tutorial of the
usage of the CGenFF for construction ITP topology for charmm f.f ?


Also I still could not found any simple way to monitor dynamics of the
non-covalent interactions between ligand and ligand binding pocket.
E.g I select manually in the ndx file all residues which could be
involved in such interactions (including formation of  possible
h.bonds, salt bridges as well as stacking interactions ) in one group
and ligand inthe second group. Should I use combination of g_hbond and
g_saltbr tools for such identification? How stacking interactions
could be monitored?


James

2013/2/5, James Starlight <jmsstarlight at gmail.com>:
> 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
>