RE: AMBER: minimize a ptraj average pdb structure

From: Bill Ross <>
Date: Wed, 9 Feb 2005 11:39:27 -0800 (PST)

> >Hi, I have obtained an average structure for a protein
> >in water. Now the question is how to minimize the
> >average structure. I suppose that I should limit the
> >number of steepest descent (NCYC) while keeping the
> >average water molecule. Can people give some
> >suggestions based on their experience?

If your trajectory ran any appreciable amount of time, the waters
will need to be discarded.

> Since you don't want the structure to change that much, in my opinion you
> could simply control it by switching rmsd of gradients....another opinion is
> to proceed with a gradual progressive minimization, like minimizing first
> hydrogens, then side chains and then all the solute with backbone fixed by a
> force constant. In this last step you could choose an RMSD value say
> 0.1......and not will then have just a clean structure,
> without any bumps, that is perhaps you need..

The same 500 steps of steepest descent that one would normally
use to prepare for initial dynamics will probably suffice.

Unless there were major motions that result in average positions
that involve, say, bonds threading through rings or the like. Which
is the sort of thing that may be found with the waters.

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Received on Wed Feb 09 2005 - 19:53:01 PST
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