AMBER Archive (2006)

Subject: AMBER: H-bonds of peptide with water

From: sangeeta (
Date: Fri Aug 04 2006 - 08:20:13 CDT

Dear Amber Community,
I am trying to analyse h-bonds formed between atoms of peptide and water
during MD trajectory. When I run the Ptraj script attached herewith, I get
only the intramolecular H-bonds in the peptide. No peptide-solvent H-bonds
are reported in the output (also attached here). I would appreciate help
reg. this. Is my script wrong somewhere? (It is a modified version of the
script available in Amber Tutorial 8).

This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to