Re: [AMBER] Minimization Failure

From: Bill Ross <>
Date: Tue, 16 Mar 2010 11:36:17 -0700 (PDT)

> but can i do something about this, for example open the
> prmtop file or the inpcrd file and 'somehow' find atom 4615 and change
> its position?

Technically you could do the math to figure out which numbers
in the inpcrd to change (consider each atom has x, y, z coords).
Or you could generate a pdb and look at it to actually understand
what the problem is, posssibly fixing it and regenerating prmtop
and inpcrd.

What I'd be inclined to try is some 10K dynamics (with SHAKE)
to see if that will get you over the problem. You might even
go on to start your equilibration from there.


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Received on Tue Mar 16 2010 - 12:00:03 PDT
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