AMBER Archive (2007)

Subject: Re: AMBER: Restraining valence angles

From: David A. Case (case_at_scripps.edu)
Date: Wed Jun 06 2007 - 09:49:08 CDT

On Wed, Jun 06, 2007, Abi Ghanem josephine wrote:

>
> I am trying to restrain some valence angle in a DNA dynamic.
> The problem is the restraint are not tooken in account,
> at first my restrain where at 2Kcal and i raied them till 100, but still
> the angles are not following the restraint file.
> i checked in the out file, the restraint are all taken in account.

The output file will show each of the angles, what its actual value is,
and what energy was applied. (Set pencut=-1. to see even zero restraint
values.) Studying this should help you understand what is happening.

>
> #20 THY : (20 DT O5')-(20 DT O3')-Na+ 69.0 83.0
> &rst iat = 604, 632, 909,
> r1 = 68.50, r2 = 69.0, r3 = 83.00, r4 = 82.50,
                                  ^^^^^^^^^^^^^^^^^^^^^^^^

Please be sure that r1 < r2 <= r3 < r4. I'm not sure what happens when
you violate this requirement.

> nstlim=100000, t=0.0, dt=0.002,
   ^^^^^^^^^^^^^^^^

run a short (10 step simulation), print results at every step; set LISTIN=POUT
to get more information. You can run a long simulation later, once you are
confident you understand what is going on.

.....dac

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