On 1/22/18 5:58 AM, Seera Suryanarayana wrote:
Dear gromacs users,
I have done simulations of 20 residue length of peptide for 100ns. I want
to find hydrogen bonds for residue GLU-7. The topology information for
this residue as follow.
; residue 7 GLU rtp GLU q -1.0
121 opls_238
Thanks, I will try this option too. But now I would want to look at the
particular hydrogen bonds between protein and ligand if these h bonds are
present after the simulations. So, please let me know how can I interpret this
data that I sent? ---
On Saturday, 4 July 2015 11:49 AM,
Hi,
the -hbn option in g_hbond in connection to your issue of determining
the hydrogen bond lifetime or stability does not tell you much. What you
should be looking at is running the g_hbond with -ac flag which gives you
the lifetime and H-bond formation energy between two groups specified by
On 7/4/15 3:05 AM, Dr. Seema Mishra wrote:
Thanks, I will try this option too. But now I would want to look at the
particular hydrogen bonds between protein and ligand if these h bonds are
present after the simulations. So, please let me know how can I interpret this
data that I sent? ---
As a said the -hbn option in g_hbond is probably not informative in your
case. First tell us what do you really want to observe? The no. of hydrogen
bonds between specific amino acid residues and your ligand binding sites?
If yes, use g_hbond with -num option that will give you the exact no of
I found one problem. If I create new group in index.ndx file which contains
protein without CH6 residue then some h-bonds are detected but actually I
wouldn't expect it the way it looks.
So again, how does actually g_hbond calculate hydrogen bonds except the
distance and angle restraints. Does it
On 8/20/14, 12:02 PM, Dawid das wrote:
I found one problem. If I create new group in index.ndx file which contains
protein without CH6 residue then some h-bonds are detected but actually I
wouldn't expect it the way it looks.
So again, how does actually g_hbond calculate hydrogen bonds except
Hi,
You need to inspect the -hbm and -hbn output. It's the complete existence
matrix for all h-bonds encountered in the analysis and a list of corresponding
acceptor-H-donor triads. Consequently those files are usually rather big, but
that's where the information is. Inspect the bonds you find
On 5/28/14, 12:59 AM, bharat gupta wrote:
Hi,
I want to find the interacting hydrogen bonding residues with the residue
of my choice. I made an index for the residue for which I want to find the
hydrogen bonds and I get the number of hydrogen bond it makes during the
simulation. But how can I
