Hi,
I recently added this feature to GitHub cpptraj (version 6.4.5). Let
me know if it works for you if you get a chance to try it. More
details here: https://github.com/Amber-MD/cpptraj/pull/960
-Dan
On Wed, Mar 16, 2022 at 9:45 AM Matthew Guberman-Pfeffer
<matthew.guberman-pfeffer.uconn.edu> wrote:
>
> Dear Amber Community,
>
> I need to quantify the total number of H-bonds for each pair of residues in my protein. That would mean a 1321 x 1321 matrix. I am having trouble in writing a bash script to process the CPPTRAJ hbond output (e.g. All.UU.avg.dat) to compute each matrix element. I’ve thought of running CPPTRAJ for every possible pair of donormask and acceptormask, but this is truly an ugly brute-force approach. Does anyone have suggestions on how I can compute the total number of H-bonds between each pair of residues?
>
> Best,
> Matthew
>
>
>
>
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Received on Wed Mar 30 2022 - 13:00:02 PDT
