[Dock-fans] AMBER: Puzzle with WAT

Francesco Pietra chiendarret at yahoo.com
Sun Nov 18 00:09:27 PST 2007

Thank you, finally clear. Though it is not clear why my turnaround (ambpdb)
removed the bond, or, in other words, made valency correct for dockprep (which
was needed for dockprep to work; in fact, the issue was raised just by dockprep
finding valency problems). Because DOCK and AMBER must be run in alternation,
do you have any suggestion how to deal with? Perhaps use other than TIP3 for
just that molecule and TIP3 for the water molecules mixed with POPC?

Another question. I did not separate with TER the water molecules mixed to POPC
in the membrane. top and crd were obtained. Correct?


--- Bill Ross <ross at cgl.ucsf.edu> wrote:

> Water has an H-H 'bond' so that the SHAKE algorithm can keep it rigid,
> which is required for TIP3P.
> Bill
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