VMD-L Mailing List

From: Sadegh Faramarzi Ganjabad (safaramarziganjabad_at_mix.wvu.edu)
Date: Mon Jun 05 2017 - 15:27:57 CDT

Hello VMD users,

I am calculating hbonds for a detergent in aqueous solution using hbond
plugin of VMD. Say I have 5 oxygen atoms in the detergent molecule. Some of
them can be only acceptor and some can be either donor or acceptor or both.
To get the total hbonds I put all oxygen atoms in 'Selection 1" and and
specified them as both donor and acceptor. The total number of hbonds per
detergent is ~3.

Then I calculated hbonds for the oxygen atoms separately. For the donors I
told VMD that it is donor only. For the ones that can be both donor and
acceptor, again I calculated them separately (in one set I told VMD that
they are only donor, in the another set I told it that they can be only
acceptors. 'Selection 2' was the rest of oxygen atoms). The sum is 4.7
hbonds per detergent. Does anybody know why it happens? all other options
are the same for all sets.

Thanks,
Sadegh