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.N solvent acceptor 70 3.341 (0.13) 43.63 (11.16)
solvent donor 558.H 558.N 60 2.8 (0.13) 33 (13)
I could like to ask how can confirm if the 561.N and 558.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,
Cat
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Received on Mon Jul 06 2009 - 10:01:38 PDT
