Dear AMBER community,
I am trying to set up a control system where *molecule 1 *(*M1*) should not
interact with *ion 1 (I1)*. When keeping I1 in bulk, during the
simulations there is an M1-I1 inclusion complex formation.
I wanted to set up a control system so that there is no overall interaction
between M1 and I1. After scanning through the AMBER archive, I found that
distance restraint could be helpful. I tried to maintain a minimum distance
of 5 Angstrom between M1 and I1 using the following script.
###
&cntrl
imin=0, ntx=7, ntpr=50, ntwr=2500, ntwx=25000,
nscm=5000,
ntf=2, ntc=2,
ntb=2, ntp=1, tautp=5.0, taup=5.0,
nstlim=25000000, t=0.0, dt=0.002, nmropt=1,
cut=9.0,
ntt=1,
iwrap=1,
irest=1
/
&wt
type='DUMPFREQ', istep1=50, /
&wt
type='END',
&end
DISANG=restraints.dat
###
###The content of restraints.dat file:
&rst
iat=-1,-1,
r1=0.0, r2=5.0, r3=5.0, r4=40.0, rk2=10.0, rk3 =0.0001,
igr1=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,
igr2=77,
&end
##
Where M1 (atom: 1-76) and I1 (atom: 77) should be at least 5 Angstrom
apart.
I found that during simulations the inclusion complex still forms and the
output file reads:
"RESTRAINTS:
No valid redirection requests found
** No restraint defined **"
###
I believe something is not correct with the script and the restraining is
not working.
So, I would like to ask:
1. Am I using a correct approach to achieve no interaction between M1 and
I1 during the course of simulations?
2. If using distance restraints is the right approach, how to correct my
input script.
Any help would be highly appreciated!
Thanks and best,
Jac
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Received on Mon Apr 19 2021 - 02:30:02 PDT
