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 l
ve the pdb. 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
&g
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 n
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 maili
: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
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 m
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 c
On Saturday, 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-li
, 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 wi
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
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