AMBER Archive (2009)

Subject: [AMBER] question with hbond

From: Ganesh Kamath (
Date: Wed Sep 16 2009 - 16:36:18 CDT


 I am trying to use hbond in ptraj and want to find the neighbouring water
hbonding with the donor here OE1 (oxygen)

trajin data-0.00.crd
center origin
image origin center
donor mask @3535
hbond series hbond hbond_wat.out solventdonor WAT O solventacceptor WAT O H1
solventacceptor WAT O H2 time 1.0 angle 120.0 distance 3.5

I use these set of command and I get segmentation fault. It also asks me to
increase the solventneighbor which i increase to 100.

Could anyone please help me on this.

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