AMBER: hbond ptraj

From: Catein Catherine <>
Date: Thu, 17 May 2007 11:39:02 +0800

Dear Sir/Madam,

I could like to analysis all hydrogen bond between a drug with the protein
during the simulations time.
I setup the ptraj file as below:

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

Did I do anything wrong here?

Best regards,


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