AMBER Archive (2009)

Subject: RE: [AMBER] Re: force units

From: Catein Catherine (
Date: Thu Jun 18 2009 - 09:01:40 CDT

Dear Sir/Madam,


I finished a 3ns simulation for a system. I used ptraj to identify H-bond involved in the residues around the active sites. I found the results output as follows:


DONOR ACCEPTORH ACCEPTOR occupied distance angle

561_at_N solvent acceptor 70 3.341 (0.13) 43.63 (11.16)

solvent donor 558_at_H 558_at_N 60 2.8 (0.13) 33 (13)


I could like to ask how can confirm if the 561_at_N and 558_at_H is connected by a water-mediated hydrogen bond. Is it possible to identify the flexibility and correlated motion of this mediated water? How can I indentify atom number of this solvent?


Best regards & thanks,



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