> 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).
The bond is only present in the prmtop file. Only programs that load that
file will see it. Once you output to pdb, the only programs that show a bond
will be those that have their own model of water having an H-H bond.
> 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?
Since the bond is effectively stripped outside of amber, you shouldn't
need to worry about it.
> Another question. I did not separate with TER the water molecules mixed to POPC
> in the membrane. top and crd were obtained. Correct?
Not sure - haven't used amber for a while; I think I used TER before. I
would add TERs to be on the safe side.
Bill
>
> --- Bill Ross <ross.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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Received on Wed Nov 21 2007 - 06:07:09 PST
