On 10/4/19 12:11 PM, Pandya, Akash wrote:
Hi all,
This may sound like a stupid question, but is there a "selection process"
within gromacs whereby I can determine the correct donor-acceptor distance and angle
cut-offs for hydrogen bond analysis for my protein-ligand. Just glancing various
Hi all,
This may sound like a stupid question, but is there a "selection process"
within gromacs whereby I can determine the correct donor-acceptor distance and
angle cut-offs for hydrogen bond analysis for my protein-ligand. Just glancing
various literature that study protein-water/
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
On 6/19/17 3:49 AM, João Henriques wrote:
Dear Imrul,
I believe the information you seek is right there in your xvg file header:
@xaxis label "Time (ns)"
@yaxis label "Number"
...
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"
First column is always time
Dear Imrul,
I believe the information you seek is right there in your xvg file header:
@xaxis label "Time (ns)"
@yaxis label "Number"
...
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"
First column is always time (x-axis). All other columns are y-axes for
different
Dear all
For hydrogen bond analysis, we generate *.xvg file for -num tag in gmx
hbond command. My inquiry is in the xvg file there are three column
output. First column is time. Which one is hydrogen bond number?
If number 2 column is hydrogen bond number in every frame than what is
number 3
Dear all
I wish to analyze hydrogen bonds in a gromacs MD trajectories with g_hbond. I
want to get information about the life time of individual hbonds between the
receptor and ligand in the structure through the trajector. in the output log
file of g_hbond command, I can find the list of
