Dear all
I am not sure if I have implemented parabolic restraints correctly. If I want to extend a distance by 2 A0(for example, from 10 A0 to 12 A0) by the application of parabolic restraints, How do I implement that using nmropt?
Is the following correct to apply the parabolic restraints to extend it from 10A0 to 12 A0:
&rst
iat=A,B,
r1=0,
r2=10.0,
r3=12.0
r4=9999,
rk2=100.0,
rk3=100.0,
/
Then, I don't understand why in the manual it says R(the value of the restraint) can be equal to either r1 or r3? I thought that, for parabolic restraints, we normally set r1=0, r4=999(9), then r2 would be the current length(or distance between the two masks), and r3 would be the target length(or target distance between the two masks)??
I would appreciate if you also tell me what the value of R or the value of the restraint would be based on the numbers in the example above?
Thanks for your input
Ramin
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 27 2017 - 02:30:03 PDT
