Re: [gmx-users] HYDROGEN BOND EXISTENCE MAP

Thanks. On Sat, Apr 1, 2017 at 12:59 PM, Sheeja Vasudevan wrote: > > Hi Neha, > > If I understand correctly pdb file is used for extracting information > about the topology of the molecule..in this case the atom name and type. > so it does not matter at which time point of

Re: [gmx-users] HYDROGEN BOND EXISTENCE MAP

Hi Neha, If I understand correctly pdb file is used for extracting information about the topology of the molecule..in this case the atom name and type. so it does not matter at which time point of time in your simulation your pdb file is generated as long as it is whole molecule. Best Sheeja.

[gmx-users] HYDROGEN BOND EXISTENCE MAP

Hi gromacs users, In the perl script to calculate hydrogen bond %, the command is perl plot_hbmap.pl -s structure.pdb -map hbmap.xpm -index hbond.ndx What should the structure.pdb file contain? How to obtain it? At which point of simulations? Thanks, Neha -- Gromacs Users mailing list *

[gmx-users] Hydrogen bond existence map

Hi all I would like to create hydrogen bond existence map for interaction of each residue with my ligand. I am aware that -hbm and -hbn option of g_hbond along with index file would serve the purpose. But the resulting output file is giving existence map for each atom of the residue. Instead, I

Re: [gmx-users] Hydrogen bond existence map

Hi Nidhi, Only with post processing of named files I'm afraid. Kind regards, Erik On 19 Jun 2014, at 10:48, Nidhi Katyal nidhikatyal1...@gmail.com wrote: Hi all I would like to create hydrogen bond existence map for interaction of each residue with my ligand. I am aware that -hbm and -hbn