AMBER Archive (2007)

Subject: Re: AMBER: restraint_wt and fixing chi

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Thu May 10 2007 - 12:09:59 CDT

> Thank you for all the help. I am able to restrain atom movement now. I just
> wanted to know what is tha maximum value of restraint_wt that can be applied
> in amber9? Is there any limit to it?

You can set it as high as you want; of course, the higher you set it, the
higher the frequency of the vibration and therefore the smaller time step
you must apply (in dynamics). In practice, I tend to use force constants
in the range of 0.5-5.0 kcal/mol-A2.

> Also, I would be grateful if somebody can tell me how to fix angles at
> partiuclar values. like if i want to set chi to some value. I searched the

You cannot easily "fix" or constrain dihedral angles to a particular
value in current implementations; you can restrain them. The input you
supplied looks on the right track, however I would increase the range for
the "harmonic" penalty,

 &rst iat = 1, 5, 21, 23,
          r1 = -195.0, r2 = -180.0, r3 = -180.0, r4 = -165.0,
          rk2 = 2.0, rk3 = 2.0, &end

Finally, as often mentioned on this list, run a short simulation to try it
out (i.e. the different restraints, force constants, etc) and see if you
see the expected behavior...

-- tec3
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