AMBER Archive (2009)

Subject: Re: [AMBER] ambpdb water removal for rst files

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Sun Dec 06 2009 - 14:09:26 CST

> > maybe it s posible to strip waters from .rst file and then convert
> > it to PDB.
> Ideally someone (it could be you) would add a -nowat option to
> ambpdb to do the right thing.

PS - stripping from rst means you'd have to generate the no-wat
prmtop for ambpdb to work with the modified rst. Making the change
to ambpdb is more sensible I think. While at it, a -nosolvent flag
could strip whatever prmtop thinks is solvent (there is a pointer
to the solvent section as I remember), which might provide
the convenience of leaving in xtal waters.

Bill

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