Re: [gmx-users] Hydrogen bond occupancy

Hi, On Wed, Apr 5, 2017 at 1:09 PM Neha Gupta wrote: > Hi, > > Thank you for the reply. > > However, I don't get the same bonds as obtained through docking. Those > hydrogen bonds have vanished, I presume during the simulation duration of > 2ns. > Sounds like it.

Re: [gmx-users] Hydrogen bond occupancy

Hi, Thank you for the reply. However, I don't get the same bonds as obtained through docking. Those hydrogen bonds have vanished, I presume during the simulation duration of 2ns. The bonding takes place with different protein residues. One donor - acceptor has higher percentage (29%) and the

Re: [gmx-users] Hydrogen bond occupancy

Dear Neha, What fraction of the time the ligand hydrogen bonds to whatever it interacts with. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539

[gmx-users] Hydrogen bond occupancy

Hi gromacs users, What is meant by Hydrogen bond occupancy in protein ligand simulations? What information do we extract from % of hydrogen bond occupancy? Thanks, Neha -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List