AMBER Archive (2002)

Subject: DNA structure get distorted

From: Monica (monicdbs_at_iitr.ernet.in)
Date: Thu Apr 11 2002 - 03:00:48 CDT

Dear Amberites,
I am running Simulated Annealing on DNA hexamer.My input
file is:
----------------------------------------------------------------------------
simulated annealing protocol, 63.5 ps

 &cntrl
    imin=0, ntx=1, nstlim=63500,
    temp0=100.0, tempi=100.0, igb=3
    ntt=1, ntb=0, ntf=1, nmropt=1, vlimit=20,
    ntpr=1000, ntt=1, ntwx=2544, ntwv=2544, ntwe=2544,
    cut=10.0, scee=1.2,
 &end
#
#Simple simulated annealing algorithm:
#CHANGING WEIGHT INF FOR TOR & VDW
#
 &wt type='TORSION', istep1=0,istep2=34000,value1=20.,
            value2=20., &end
 &wt type='TEMP0', istep1=0,istep2=1000,value1=100.,
            value2=300., &end
 &wt type='TEMP0', istep1=1001,istep2=2000,value1=300.,
            value2=300., &end
 &wt type='TEMP0', istep1=2001,istep2=3000,value1=300.,
            value2=500., &end
 &wt type='TEMP0', istep1=3001,istep2=4000,value1=500.,
            value2=500., &end
 &wt type='TEMP0', istep1=4001,istep2=5000,value1=500.,
            value2=700., &end
 &wt type='TEMP0', istep1=5001,istep2=6000,value1=700.,
            value2=700., &end
 &wt type='TEMP0', istep1=6001,istep2=7000,value1=700.,
            value2=900., &end
 &wt type='TEMP0', istep1=7001,istep2=8000,value1=900.,
            value2=900., &end
 &wt type='TEMP0', istep1=8001,istep2=9000,value1=900.,
            value2=1000., &end
 &wt type='TEMP0', istep1=9001,istep2=34000,value1=1000.,
            value2=1000., &end
 
&wt type='TORSION', istep1=34001,istep2=67000,value1=20.,
            value2=40., &end
 &wt type='TEMP0', istep1=34001,istep2=35000,value1=1000.,
            value2=900., &end
 &wt type='TEMP0', istep1=35001,istep2=36000,value1=900.,
            value2=900., &end
 &wt type='TEMP0', istep1=36001,istep2=37000,value1=900.,
            value2=800., &end
 &wt type='TEMP0', istep1=37001,istep2=38000,value1=800.,
            value2=800., &end
 &wt type='TEMP0', istep1=38001,istep2=39000,value1=800.,
            value2=700., &end
 &wt type='TEMP0', istep1=39001,istep2=40000,value1=700.,
            value2=700., &end
 &wt type='TEMP0', istep1=40001,istep2=41000,value1=700.,
            value2=600., &end
 &wt type='TEMP0', istep1=41001,istep2=42000,value1=600.,
            value2=600., &end
 &wt type='TEMP0', istep1=42001,istep2=43000,value1=600.,
            value2=500., &end
 &wt type='TEMP0', istep1=43001,istep2=44000,value1=500.,
            value2=500., &end
 &wt type='TEMP0', istep1=44001,istep2=45000,value1=500.,
            value2=400., &end
 &wt type='TEMP0', istep1=45001,istep2=46000,value1=400.,
            value2=400., &end
 &wt type='TEMP0', istep1=46001,istep2=47000,value1=400.,
            value2=300., &end
 &wt type='TEMP0', istep1=47001,istep2=67000,value1=300.,
            value2=300., &end
 &wt type='REST', istep1=0,istep2=34000,value1=1.0,
            value2=3.0, &end
 &wt type='REST', istep1=34001,istep2=67000,value1=3.0,
            value2=5.0, &end
 &wt type='END' &end
LISTOUT=POUT
DISANG=owncgalldist
-------------------------------------------------------------------
but finally when I view structure it is distorted.
can anyone suggest what is the reason.
I will be very grateful for your help.

Monica
Deptt Biosci Biotech
IIT,Roorkee
India