Hi,
On Wed, Feb 18, 2015 at 8:42 AM, Ayesha Fatima <ayeshafatima.69.gmail.com>
wrote:
> the postings between George and yourself, I figure it is possible to
> specify residues from residues and ligands but if the residues are not in
> series how can we specify them.
The easiest way to choose out specific hydrogen bond time series for
subsequent analysis is to make sure you write the time series data to a
file after your run like so:
hbond H1 series .N,H,C,O
go
writedata solutehb.dat H1[solutehb]
This can then be read in later on with 'readdata'. If there is no time
series generated for the hydrogen bond you are looking for and you are sure
you defined your acceptors and donors correctly that means there was no
hydrogen bond according to the distance/angle criteria that was specified.
> another thing is the interpretation of the
> output.if the line reads
> ZER_568.O1 GLN_261.H GLN_261.N 125 0.0050 0.9408
> 148.6712
>
> Does this mean that the residue ZER is the acceptor, and GLN 261 H is the
> donor, the bond exists for 125 frames with an average distance of 0.948. So
> what is the lifetime of the bond?
>
This output is explained via the file header and in the manual. You can't
get lifetime information from this output, you need to use the time series
data and the 'lifetime' command like so (could be e.g. right after the
above input):
lifetime H1[solutehb] out life.dat
Please consult the manual for more details on 'lifetime' analysis. Hope
this helps,
-Dan
> Thank you
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>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Feb 18 2015 - 08:30:02 PST
