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 <jmsstarli...@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 > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists