Re: AMBER: Atoms restrain

From: David A. Case <>
Date: Mon, 19 Dec 2005 08:20:25 -0800

On Mon, Dec 19, 2005, Angelo Pugliese wrote:
> Below there is the input file for a MD equilibration step in which I
> want to restrain my 24 residues dsDNA with 5.0 kcal/mol weight and let
> the water molecules and the counterions be free to move. Within the DNA
> I want to restrain four C1' atoms with a different weight (10.0) in
> order to keep the helix overtwisted as I set previously by nucgen.
> I wonder if my input file is correct, i mean I am afraid that the
> restrain on the whole DNA will overwrite the restrain on the single
> atoms and therefore messing up everything.

I think the second set of restraints will override the first; you could look
at the code and/or add some print statements to check this. (Easier, make
restraints that only affect one or two atoms, and experiment to see what

However, there is no practical difference between a restraint weight of 5 and
one of 10. They are both very strong, and will essentially keep the system
from moving more than a tenth of an Angstrom or so for the initial positions.
So this particular run is probably not going to make any real progress toward


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Received on Mon Dec 19 2005 - 16:53:00 PST
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