Dear AMBER list,
I want to apply repulsive restraints between two ligands to prevent them
from aggregating. I use the CUDA version 12.3 and hence I cannot apply
forces to atom groups. Therefore I tried to adapt the typical parabolic
well restraint to apply a repulsive force on a single atom of each ligand.
&rst
ialtd=0, ! the penalty energy continues to rise for large violations
ir6=1, ! no center of mass averaging will be used
iresid=0, ! IAT(I) points to an atom number (atom ID)
iat=2855,2993, ! the distance between these two atoms will be used
! the restraint is a well with a square bottom with
parabolic sides out to a defined distance, and then linear sides beyond
that.
! If R is the value of the restraint in question:
r1=0.0, ! R < r1 Linear, with the slope of the "left-hand" parabola
at the point R=r1.
r2=40.0, ! r1 <= R < r2 Parabolic, with restraint energy k2(R-r2)^2.
r3=2000.0, ! r2 <= R < r3 E = 0
r4=2500.0, ! r3 <= R < r4 Parabolic, with restraint energy k3(R-r3)^2.
! r4 <= R Linear, with the slope of the "right-hand"
parabola at the point R=r4.
rk2=20.0, ! force constant k2 (see above)
rk3=20.0, ! force constant k3 (see above)
&end
Basically, I prevent attractive restraints between the ligands by setting
r3 and r4 to very high values. However, I don't see any repulsion happening
in the trajectory. Is my rationale correct? Is there any more effective and
elegant way to apply repulsive restraints to the ligands?
thanks in advance,
Thomas
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Thu Mar 27 2014 - 09:00:02 PDT
