I wouldn't say wrong, but I realized that some residue may make two
hbonds to different parts of the protein, i.e. to the main chain and
to a side chain at the same time. With -merge this counts as one if
you analyze the entire protein. If you split your analysis such hbonds
will show up in both e.g. SS and MS, hence TOT < MM+SS+MS. It's just
another way of counting hbonds.
Erik
On Mar 22, 2013, at 5:32 PM, Kavyashree M wrote:
Sir,
I tried -nomerge. It is fine now. But will it be wrong to
calculate without nomerge option?
Thank you
Kavya
On Fri, Mar 22, 2013 at 9:28 PM, Erik Marklund
<er...@xray.bmc.uu.se> wrote:
I could see how -merge (on by default) could lead to this. Have you
tried
-nomerge?
Erik
On Mar 22, 2013, at 4:46 PM, Kavyashree M wrote:
Dear Users,
As suggested earlier by Erik I used 4.6 to calculate the hydrogen
bonds.
Still the
Total intra-protein hydrogen bonds is not equal (MM +MS +SS)
hydrogen
bond.
Is there any other solution?
Thank you
Kavya
On Fri, Jan 25, 2013 at 4:11 PM, Kavyashree M <hmkv...@gmail.com>
wrote:
Dear Sir,
Sure I will try with 4.6. presently I am not able to download it.
Thank you
kavya
On Fri, Jan 25, 2013 at 4:04 PM, Erik Marklund
<er...@xray.bmc.uu.se
wrote:
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 <er...@xray.bmc.uu.se
>
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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