AMBER Archive (2006)

Subject: RE: AMBER: some puzzles in equilibration MD

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Oct 09 2006 - 22:14:39 CDT

> Alternatively you can write a pdb file from the prmtop and inpcrd files and
> then load this into a program that allows you to manually move atoms by
> hand. Then you can write this back as a pdb file, feed it into leap and
> create a new prmtop and inpcrd file. Assuming of course that the
> manipulation program you choose doesn't mangle the pdb format. Unfortunately
> I don't know of any free programs that do this off hand. Perhaps someone
> else on the list knows of some useful ones.

Or you can find and move atoms in xleap, also do minimizations
on groups of atoms selected by mouse.

Bill
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