AMBER Archive (2006)

Subject: AMBER: H-bonds of peptide with water

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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).
Thanks.
Sangeeta

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• text/plain attachment: hbond_peptclost_wat_gen.trajin

• text/plain attachment: cgaslv10ns_trj_hbond.dat

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• Next message: Gloria T. Anderle: "AMBER: Residue connection points on prep.in"
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