Re: [gmx-users] Generate diagram/figure with information about protein-ligand interactions

The figure is generated using Desmond. Check the following paper: http://dx.doi.org/10.1016/j.bmc.2014.02.020 On Thu, Mar 31, 2016 at 4:34 PM, Tsjerk Wassenaar wrote: > Hi biohpc, > > For this you need to combine output from gmx hbond, gmx sasa, and gmx > saltbr. > > Cheers, > > Tsjerk > On Mar

Re: [gmx-users] Generate diagram/figure with information about protein-ligand interactions

On 3/31/16 6:58 AM, bio hpc wrote: My problem is not excel or whatever graphical program. I just need the data, in an automatic way. Then I can use either matplotlib or similar to get the plots automatically. But my question is if there is somewhere a repository of gromacs scripts with a script

Re: [gmx-users] Generate diagram/figure with information about protein-ligand interactions

Hi biohpc, For this you need to combine output from gmx hbond, gmx sasa, and gmx saltbr. Cheers, Tsjerk On Mar 31, 2016 12:58, "bio hpc" wrote: > My problem is not excel or whatever graphical program. I just need the > data, in an automatic way. Then I can use either matplotlib or similar to >

Re: [gmx-users] Generate diagram/figure with information about protein-ligand interactions

My problem is not excel or whatever graphical program. I just need the data, in an automatic way. Then I can use either matplotlib or similar to get the plots automatically. But my question is if there is somewhere a repository of gromacs scripts with a script doing an analysis of the protein-li

Re: [gmx-users] Generate diagram/figure with information about protein-ligand interactions

i am sorry, i replied prior to looking at your figure. Actually, i have never came across plotting data in this matter. However, I believe you have tabulated data, so you can use Origin or excel for generating similar images. You need little effort to arrange the data in desired manner. Best Wishes

Re: [gmx-users] Generate diagram/figure with information about protein-ligand interactions

I have not looked at your link yet but I believe PyMol is best for generating high quality figures. You can explore a number of options in pymol. Regards Suniba Sent from my iPhone > On 30-Mar-2016, at 3:15 am, bio hpc wrote: > > Hi, > > after a protein-ligand simulation with gromacs, I woul

[gmx-users] Generate diagram/figure with information about protein-ligand interactions

Hi, after a protein-ligand simulation with gromacs, I would like to be able to generate a diagram/figure with information about protein-ligand interactions, something like this: https://dl.dropboxusercontent.com/u/2012631/Figure7.jpg I