[gmx-users] Hydrogen bond analysis

Hi allI want to carry on a hydrogen bond analysis between a protein and ligand. I tested hbond but it only gives the number of hydrogen bonds which I am not looking for. I want to know exactly which residues are involved in hydrogen bonding and more specifically which atoms of the residues and

Re: [gmx-users] number of coordinates in coordinate file does not match topology

. Use pdb2gmx to recreate the top.  good luck > On 16,May 2019, at 1:13 PM, mary ko wrote: > > Hello all > I want to run a simulation of a protein from PDB data bank with a ligand. It > has two chains and I need only chain A. when I delete chain B in CHIMERA and > try to

[gmx-users] number of coordinates in coordinate file does not match topology

Hello all I want to run a simulation of a protein from PDB data bank with a ligand. It has two chains and I need only chain A. when I delete chain B in CHIMERA and try to run the simulation, it stops at the gmx_mpi grompp -f ions.mdp -c solve.pdb -p topol.top -o ions.tpr step with the error of

[gmx-users] protein-ligand analysis

Hi all How can I find the chains interacting, forming H-bonds and hydrophobic interactions after a protein-ligand simulation? I tried VMD but there seems not to be good options to characterize them all. Is it possible to do such analysis in VMD or Gromacs and how? Thanks. -- Gromacs Users

Re: [gmx-users] VMD movie making-remove water molecules from .trr after a simulation

:32:22 PM EDT, Justin Lemkul wrote: On 3/11/19 6:01 PM, mary ko wrote: > Dear all > How can I make a movie from a protein-ligand simulation in VMD? I opened > complex.pdb and md-fit.trr and  the movie is shown but due to the large > number of water molecules it freezes after

[gmx-users] VMD movie making-remove water molecules from .trr after a simulation

Dear all How can I make a movie from a protein-ligand simulation in VMD? I opened complex.pdb and md-fit.trr and  the movie is shown but due to the large number of water molecules it freezes after some frames. How can I remove solvent molecules from the md-fit.trr? Any other suggestions how to

[gmx-users] VMD visualization is failed

Dear all I have simulated a protein-ligand system and the md.xtc and md.gro are now generated in the output. Unlike my previous simulations of nano systems in which the .trr trajectory was in the output and the visualization could be done in an straight forward way of opening the .gro and .trr

Re: [gmx-users] Residue BGC not found in the database

rday, February 23, 2019, 6:50:39 PM EST, Justin Lemkul > wrote: >  >  > > On 2/20/19 11:19 AM, mary ko wrote: >> Dear all, >> I face the 'Residue BGC not found in the database' error when I try to build >> the topology file of my protein-ligand system by p

Re: [gmx-users] Residue BGC not found in the database

, Justin Lemkul wrote: On 2/20/19 11:19 AM, mary ko wrote: > Dear all, > I face the 'Residue BGC not found in the database' error when I try to build > the topology file of my protein-ligand system by pdb2gmx -f pro.pdb. I used > Charmm force field but I tried it with all the

[gmx-users] Residue BGC not found in the database

Dear all, I face the 'Residue BGC not found in the database' error when I try to build the topology file of my protein-ligand system by pdb2gmx -f pro.pdb. I used Charmm force field but I tried it with all the other force fields as well to see if the problem could be solved which was useless. I