On Sun, Jun 8, 2014 at 5:41 PM, Arunima Shilpi <writetoash28.gmail.com> wrote:
> Dear Sir
>
> I did run cpptraj command in order get the details of donor and acceptor
> groups.
>
> Further I did run ptraj command to get the details for h-bond occupancy.
Note that you can also perform lifetime analysis with cpptraj; it is
implemented as the separate analysis command 'lifetime' (as long as
you use the 'series' keyword with 'hbond'), e.g.
parm DPDP.parm7
trajin DPDP.nc
hbond H1 series .N,H,C,O
go
runanalysis lifetime H1[solutehb] out lifetime.dat
See the manual for further details. You may also be interested in the
'nointramol' keyword for 'hbond' if you want to only calculate
intermolecular hydrogen bonds.
Hope this helps,
-Dan
PS - 'lifetime' is implemented as a separate command so that it can be
used with any data sets, not just those from 'hbond'.
>
> I mainly want to check the h-bond occupancy between protein and ligand.
>
> Here the residue no 905 is for my ligand. However on analysis only single
> result shows the maximum occupancy while remaining heave very less
> occupancy.
>
>
> Here is the details of the analyis
>
>
> HBOND SUMMARY:
>
> data was sorted, intra-residue interactions are included,
> Distance cutoff is 3.50 angstroms, angle cutoff is 120.00 degrees
> Hydrogen bond information dumped for occupancies > 0.00
>
> DONOR ACCEPTORH ACCEPTOR
> atom# :res.atom atom# :res.atom atom# :res.atom %occupied distance
> angle
> | 7809 :497.O | 14291 :905.O10 14318 :905.H25 | 0.90 3.450 ( 0.04)
> 55.13 ( 3.47)
> | 7809 :497.O | 14290 :905.O9 14317 :905.H24 | 0.10 3.450 ( 0.03)
> 54.17 ( 6.24)
> | 14293 :905.O12 | 14292 :905.O11 14319 :905.H26 | 0.02 3.436 ( 0.00)
> 58.03 ( 0.00)
> ---------------- ---------------------------------
> -------------------------------------
>
> My question how to to do the detail analysis of protein-liagnd interactions.
>
> Regards
>
> Arunima
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
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 Sun Jun 08 2014 - 19:30:02 PDT
