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.
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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Received on Sun Jun 08 2014 - 17:00:02 PDT
