AMBER Archive (2006)

Subject: AMBER: Problems using rst distance constraints in Amber 8

From: Whitney Allen (whitneygallen_at_yahoo.com)
Date: Wed Sep 20 2006 - 13:30:05 CDT

Dear Amber users,
  I have run this code to constrain distances between atoms using Amber 7 and the restraints work well (in this case I want to constraint the distance between two atoms in four separate cases) However, when I use this same code in Amber 8 no restraints are found in my output file. Has there been a change in the input format? How should I format the distance constraints?
  Thanks
  Whitney
  
  equilibrate the structure
 &cntrl
   imin=0, ntx=5,
   irest=1, ntxo=1,cut=15.0, tempi=300.0,
   ntpr=1000, ntwx=1000, ntwe=1000,
   nstlim=4000000,tautp=2, temp0=300.0,
   dt=0.001, nscm=100,
   igb=1,ntb=0, saltcon=0.5, gbsa=1,
   ntt=1, nsnb=20,offset=0.13, ntr=0,
   nmropt=1,
 &end
  &wt
   type='END'
&end
&rst iat=19,1938,
     ir6=0,
     r1=0.0, r2=0.5, r3=4.5, r4=9.0,
     rk2=0.2, rk3=0.2,
&end
&rst iat=53,1907,
     ir6=0,
     r1=0.0, r2=0.5, r3=4.5, r4=9.0,
     rk2=0.2, rk3=0.2,
&end
&rst iat=971,1070,
     ir6=0,
     r1=0.0, r2=0.5, r3=4.5, r4=9.0,
     rk2=0.2, rk3=0.2,
&end
&rst iat=1005,1039,
     ir6=0,
     r1=0.0, r2=0.5, r3=4.5, r4=9.0,
     rk2=0.2, rk3=0.2,
&end

                                 
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