AMBER: Re: restraints

From: xiaoqin huang <>
Date: Wed, 26 Oct 2005 17:25:03 -0400

Hi, Dear amber users
could you tell me the role of r1a, r2a, r3a, r4a,(rk2a, rk3a) in the
restraints ?
from my understanding, the r1 to r4 (rk2 and rk3) are used to restrain the
distance, or angle, torsional as explained in hte manual. for example, if
the R (input) is between r1 and r2, then the force will put on R
parabolically based on rk2(R-r2)**2 and equals to 0 when R reaches r2, so
the R will target at r2.
and when ifvari>0, imult=0, the force constants will become rk2a, and rk3a,
so how will the R changes according to the changes of rk2 to rk2a?
I feel the role of set of r1a to r4a (rk2a, rk3a) has opposite role of the
r1 to r2 (rk2, rk3), but I donot understand the meaning of the r1a...set, so
my simulation is always bad.

my undstaning, for example, for a bond (A-B) to form between seperated A and
B, put a small value for rk3(the input R is between r3 and r4) and big for
rk2 (as the r2 is the target bond length), but a big value for rk3a in order
to pull the two atoms to form a bond, and a samll value for rk2a, thus can
keep the target value of the onging bond formation, is that right?

thanks a lot in advance!

all the best!



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Received on Wed Oct 26 2005 - 22:53:00 PDT
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