Hi Amber community,
I want to calculate hydrogen bondings (angles, distances, %occupied) using
ptraj. I create a trajin file where I define a list of hydrogen bond
"donors" and hydrogen bond "acceptors".
Then, type the option hbond:
hbond distance 3.5 solventneighbor 6 solventdonor WAT O solventacceptor WAT O
H1 solventacceptor WAT O H2
I run the calculation and finally, I obtain a result where there are
information about "donors", "acceptors", "acceptorsH", angles, distances and
%occupied.
In this calculation, intra-residue interactions are not included. I read that
information when I go to the HBOND SUMMARY:
HBOND SUMMARY:
data was sorted, intra-residue interactions are NOT included,
Distance cutoff is 3.50 angstroms, angle cutoff is 120.00 degrees
Hydrogen bond information dumped for occupancies > 0.00
I would like to take into account all the intra-residue interactions. How can
I include these interactions??
Thanks in advance,
Xavi Perez
Chemoinformatic
Department of Chemistry
Universitat Autonoma de Barcelona
Bellaterra, Spain
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Received on Wed Jun 30 2004 - 11:53:00 PDT
