Dear Amber users,
Is it correct that AMBER ignores all CONECT information in the pdb input?
What happens if the pdb contains the small molecules?
It happened to me that when I convert the prmtop and inpcrd files back to
pdb formatted file using "ambpdb", the structure does not look right to me
(containing wrong connection or bonds), then I also converted the
after_minimization_structure, it looked better but still contained wrong
bonds (e.g 5 connections for a C atom), and after all, my
equilibration_structure's totally wrong.
Could I ask for any help to explain how it could be? Any clue to avoid/fix
it?
Thank you.
Chinsu
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Received on Mon Feb 06 2012 - 20:30:02 PST
