AMBER Archive (2002)

Subject: pukering of DNA bases?

From: A.Madhumalar (malar_at_mbu.iisc.ernet.in)
Date: Sat Jan 12 2002 - 23:03:50 CST

Dear amber users,
   When i tried to do constrained equilibration run,i found that the bases
were found to be puckered.i don't understand why & how it is happening!? I
will be thankful for any suggestions regarding this
Here is my input

&cntrl
    nrun=2, nstlim=1000, ndfmin=6, ntcm=1,
    nscm=1, init=3, t=0, ntc=2,
    dt=0.001, temp0=20.0, tempi=0.0,
    ntx=1, ntt=1, tautp=0.10,
    tauts=0.10, ntp=1, pres0=1.0,
    comp=44.6, ntc=3, tol=0.0001, dielc=1.0,
    imgslt=0, iftres=1, imin=0,
    irest=0, ntxo=1, ntpr=50, ntwx=1000, ntwv=1000,
    ntwe=1000, ntwxm=1000, ntwvm=1000,
    ntwem=1000, ioutfm=0, ntb=2, idiel=1,
    cut=9.0, ntnb=1, nsnb=25,
    ntid=0, scnb=2.0, scee=1.2, ichdna=0,
    ntp=1, taup=0.2, ntf=3, iewald=1,
    dtemp=0.0, ntu=1, kform=1, ipol=0,
    heat=0.0, ndfmin=0, natrcm=0,
    ntr=1, ivcap=0, fcap=0.0,
 &end
   57.603 45.306 43.145 90.0 90.0 90.0
   57.603 45.306 43.145 4 0 0 0
    .000001
group no 1
500
RES 1 24
END
END

regards,
Madhu