AMBER Archive (2009)

Subject: Re: [AMBER] Sander and multiple residues

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Fri Apr 10 2009 - 11:42:36 CDT

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

If loading from a pdb, how did you prepare the pdb? Did it have
all the atoms in it? Why did you use 'combine'?

Normally one prepares a pdb w/ the config one wants and loads it
as in the demos.

Bill

        
        ________________________________
        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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