AMBER Archive (2009)

Subject: Re: [AMBER] Sander and multiple residues

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Thu Apr 09 2009 - 15:12:10 CDT

If you don't have a pdb file and choose to use 'combine', you
have to be ready to select one of the units using xleap selection
tools and drag/rotate it to where you need it.

Ideally 'combine' would not overlap the units, but this is a hard
problem - perhaps it could just create virtual boxes around them
and use these to avoid overlap, issuing a warning to clean up the
bond between the units. Note thatg leap minimization is useful but
still does not take vdw into account, so overlaps are still an issue.

Bill

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