Re: AMBER: hbond ptraj

From: Thomas Cheatham <>
Date: Wed, 16 May 2007 21:57:46 -0600 (Mountain Daylight Time)

> trajin DNA_drug.mdcrd 1 1000
> solvent
> solventdonor DRUG N1
> solventacceptor DRUG C2 H2
> solventacceptor DRUG N6 H61

What you want is donor/acceptor, not solventdonor/solventacceptor (those
are used within the hbond command to allow indistinguishability of

donor DRUG N1
acceptor DRUG C2 H2

assuming the residue is named "DRUG" which is suspicious since it is a
4-letter name.

> hbond distance 5.0 angle 120.0
> However, it comes up with an error message like this:
> PTRAJ: solventdonor DRUG N1
> Searching for solvent by residue name DRUG
> Segmentation fault

What is happening is the "solventdonor" is being interpreted as the
"solvent" command (which is a way to redefine what is solvent for the
closest command, among others...).

So, I would do:

donor DRUG N1
acceptor DRUG C2 H2
acceptor DRUG N6 H61
hbond series out hbond.dat distance 5.0 angle 120.0 \
  solventdonor WAT O \
  solventacceptor WAT O H1 \
  solventacceptor WAT O H2


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Received on Sun May 20 2007 - 06:07:16 PDT
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