AMBER Archive (2004)

Subject: AMBER: About Hbond calculations using ptraj

From: javier perez (
Date: Mon Jun 28 2004 - 12:43:37 CDT

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

In this calculation, intra-residue interactions are not included. I read that
information when I go to the 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

Department of Chemistry
Universitat Autonoma de Barcelona
Bellaterra, Spain

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