AMBER Archive (2002)

Subject: (no subject)

From: Monica (monicdbs_at_iitr.ernet.in)
Date: Thu Nov 14 2002 - 00:26:57 CST

Dear All,
I a doing simulation of Drug-DNA in water on AMBER6 using only
NOE distances as restraint .I followed tutorial of AMBER "NMR refinement
in Explicit water solvent".Minimization was OK.but when I did initial
equilibration.Water is blown. I am attaching f3ini_eq.pdb file with this
mail.What should I do to keep water intact. here is my input file for
initial equilibration:
***************************
NMR refinement in explicit water solvent
 &cntrl
   imin=0, nmropt=1, ntc=2, tol=0.000001, cut=9.0, ntpr=1000, ntb=1,
   scee=1.2, ntr=1, ntx=1, irest=0, ntt=1, temp0=300.0,
   tautp=1.0, ntpr=100, nstlim=20000, ntwr=99999, vlimit=20.0,
 &endB
 &wt type='REST', istep1=0,istep2=1000,value1=1.0,
            value2=1.0, &end
 &wt type='END' &end
LISTOUT=POUT
DISANG=cgadmhb_lessout
restrain
  5.0
RES 1 14
END
END
**********************************************
Thank you
Monica