Re: [gmx-users] Number of H bonds formed between ligand and amino acid residues

Hi Amali, gmx hbond identifies typical acceptor and donor groups by default. In fact, analysing non-standard donors/acceptors is a bit underdeveloped. What the program basically does, if memory serves me right, is to identify N and O with H bound to them, or optionally without H in case of

Re: [gmx-users] Number of H bonds formed between ligand and amino acid residues

Thank you very much for the answer. How we identify residues involving in H bonds? In index file do we have to specify them? On Tue, Jun 28, 2016 at 11:45 AM, Subhomoi Borkotoky wrote: > Hello, > > Please use the "hbond" utility in gromacs. > > gmx hbond [-f

Re: [gmx-users] Number of H bonds formed between ligand and amino acid residues

Hello, Please use the "hbond" utility in gromacs. gmx hbond [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]][-num [<.xvg>] On Tue, Jun 28, 2016 at 11:24 AM, Amali Guruge wrote: > Dear Gromacs users, > > I carried out 20 ns long MD simulation for my

[gmx-users] Number of H bonds formed between ligand and amino acid residues

Dear Gromacs users, I carried out 20 ns long MD simulation for my receptor-ligand complex using Gromacs software. Now I want to calculate number of hydrogen bonds formed in the ligand and receptor corresponding to the residue number. Can anyone help me? Thank you. -- Gromacs Users mailing list