Re: [gmx-users] Hbond occupancy

>mmousivand93 > >Dear Dr.Dallas warren > >I am going to analysis H-bond and Hbond occupancy using readHBmap,I downloaded >and extracted readHBmap.tar.gz but after typing: ./readHBmap.py -hbm hbmap.xpm >-hbn hbond.ndx -f md6.gro -o occupancy.xvg -op pairs.dat ,the message "No >hydrogen bonds

Re: [gmx-users] Hbond occupancy

What have you already tried? What results did you get? First point of call should be http://manual.gromacs.org/documentation/ In particular http://manual.gromacs.org/documentation/current/user-guide/cmdline.html There you can read through all the scripts that come with the software, how to use

[gmx-users] Hbond occupancy

Dear users I have run molecular dynamic for DNA-ligand complex and I am going to analysis H-bond and Hbond occupancy using GROMACS, I would appreciate any suggestions. Best regard -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Hbond occupancy

On 7/8/16 9:01 AM, Amali Guruge wrote: Thank you very much Eric for the answer. Could you please give information regarding to the command use in this calculation? Thank you. You can't get, e.g. % occupancy directly but the gmx hbond output (-hbn -hbm) can be post-processed with a simple

Re: [gmx-users] Hbond occupancy

Thank you very much Eric for the answer. Could you please give information regarding to the command use in this calculation? Thank you. On Fri, Jul 8, 2016 at 5:31 PM, Erik Marklund wrote: > gmx hbond > > > On 8 Jul 2016, at 12:24, Amali Guruge

Re: [gmx-users] Hbond occupancy

gmx hbond > On 8 Jul 2016, at 12:24, Amali Guruge wrote: > > Dear All, > > Can anyone know how to calculate H bond occupancy with Gromacs? > > Thank you > -- > Gromacs Users mailing list > > * Please search the archive at >

[gmx-users] Hbond occupancy

Dear All, Can anyone know how to calculate H bond occupancy with Gromacs? Thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For