There were a handful of bugfixes to g_hbond over the last year. Could
you try 4.6 or a smoking hot 4.5.5? I recognize this discrepancy form
before.
Erik
On Jan 24, 2013, at 3:59 PM, Kavyashree M wrote:
Dear Sir,
This is 4.5.3. I have not tried nomerge. I did not use
nomerge option in any of them, So if it has counted
it (Hbond b/w same donor and acceptor but with
different hydrogen) twice in one calculation then it will
be counted twice in another, So wont the result with/without
nomerge be the same?
The difference is 4-5 Hbonds..
Thank you
Kavya
On Thu, Jan 24, 2013 at 7:30 PM, Erik Marklund
<[email protected]> wrote:
Hi. What version was this? Have you tried with -nomerge?
Erik
On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote:
Dear users,
While calculating hydrogen bonds for a simulation, it
was found that the average number of intra protein
hbonds was not equal to sum of MM, MS and SS
hydrogen bonds. (MM - main chain - main chain,
MS - main chain - side chain and side chain - side
chain hydrogen bonds). There was a difference of 5
or so hbonds between intra-protein and MM+MS+SS
hbonds. why is this so?
I selected the options 7 7 for MM, 7 8 for MS and 8 8
for SS hydrogen bonds.
One clarification. nhbdist option gives 0, 1, 2, 3 and
total hydrogen bonds per hydrogen. Does this mean
that a single hydrogen involving in forming hbond with
2 different acceptors/donors at different points of time
in the trajectory.
Thanks
kavya
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