Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

Did anybody of you wrote such script or can that be found in some repository? > El 31/3/2016, a las 13:04, Justin Lemkul escribió: > > > > On 3/31/16 6:55 AM, bio hpc wrote: >> Thanks. >> Apart from this, is is there some script that keeps my original

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

eve 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 > > On Wed, Mar 30, 2016 at 3:15 AM, bio hpc wrote: > >> Hi, >> >> after a protein-ligand sim

Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

Hi, >>> >>> As suggested above, use -ignh to ignore hydrogen atoms. To use a specific >>> Histidine, you may change residue name HIS to >> HIP(Amber)/HSP(Charmm)/HISH( >>> ​OPLS​ >>> ) or HID(Amber)/HSD(Charmm)/HISD( >>> ​OPLS​ >>>

[gmx-users] Use pdb file generated with Maestro, in Gromacs

d some histidines in the binding site, and so on. Thanks, BIO-HPC -- 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 (un)subscri

[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