Dear All,
I have run 25ns of simulation using amber 12 and am interested in doing
hbond analysis of the binding site residues only. I searched round on the
mailing list and various tutorials and found some files which i modified
accordingly and used. The input file using residue names ran very well but
the input with residue numbers as given in Amber tutorial B3 is giving me
problems. it crashes without any reason at a specific step when it starts
to process the trajectories.I am attaching both the input and output files.
I would appreciate if someone could help me with how to get the data for
residues in the binding pocket and ligand only.
Thank you
Ayesha Fatima
PhD candidate UM Malaysia
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Received on Fri Feb 13 2015 - 00:00:02 PST
