From: Snehasis Chatterjee (
Date: Thu Jul 02 2020 - 15:54:47 CDT

Dear VMD users,

I am trying to calculate total number of H-bonds between two RNA strands
(segname R1 and R2) using "measure hbonds" command. To calculate total no.
of H-bonds, I have to consider segname R1 as donor and R2 as acceptor and
vice-versa. Or, if I consider just segname R1 as donor and R2 as acceptor,
it will catch all the different permutations. I am bit confused at this

Any kind of advice/ suggestions will be deeply appreciated.

Thanks in advance,
Snehasis Chatterjee