AMBER Archive (2009)

Subject: Re: [AMBER] Sander and multiple residues

From: Dan Kaps (dan.kaps_at_yahoo.com)
Date: Fri Apr 10 2009 - 07:57:54 CDT

I did load the coordinates from a .pdb file...Do you have any suggestions for avoiding the overlap?

________________________________
From: Bill Ross <ross_at_cgl.ucsf.edu>
To: amber_at_ambermd.org
Sent: Thursday, April 9, 2009 4:12:10 PM
Subject: Re: [AMBER] Sander and multiple residues

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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