Hello Sir,
here is the input for minimization
Initial minimization for 10000 steepest descent methods
&cntrl
ntx=1, irest=0, ntpr=10,
ntr=0,
imin=1, maxcyc=10000, ncyc=10000, ntmin=2,
dx0=0.1, drms=0.0001,
ntf=1, ntb=2, ntp=1,
cut=9.0, nsnb=10,
ntc=1,
&end
This is the input for equilibration run
Initial dynamics
&cntrl
ntx=1, irest=0, ntpr=100, ntwx=500,
ntf=2, ntb=2, cut=9, nsnb=10,
ntr=1,
imin=0, nstlim=250000, dt=0.002,
temp0=300.0, tempi=0.0,
ntt=1, tautp=0.5, vlimit=20,
ntp=1, pres0=1.0, comp=44.6, taup=0.2,
ntc=2, tol=0.00001,
/
Hold the solute fixed
10.0
RES 1 31
END
END
Prayagraj Fandilolu
Research Scholar,
Structural Bioinformatics Unit
Department of Biochemistry
Shivaji University, Kolhapur - 416004
(MS) India
On Sun, Oct 16, 2016 at 3:38 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Please paste your mdin file here. Perhaps starting temp is too high.
>
> Thanks,
>
> Bill
>
>
> On 10/16/16 2:10 AM, Prayagraj Fandilolu wrote:
> > Dear all,
> >
> > I am preparing a RNA system for MD simulation. The system consists of 2
> > modified RNA residues which are defined by Aduri et al.
> >
> >
> > The protocol consists of 1. prior minimization 2.Equilibration 3.
> > Minimization 4. Production MD
> >
> > I am getting a problem after the 1st minimization step when i try to go
> for
> > equilibration commands. The job get abnormally terminated. Also, i
> checked
> > the output PDB of the rst file which shows distorted residues.
> >
> > The mdout file shows something like this:
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > * NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
> > -6863.0 Etot = -85749.1605 EKtot = 0.0000 EPtot =
> > -85749.1605 BOND = 41.7370 ANGLE = 283.5417 DIHED
> > = 717.1987 1-4 NB = 316.9032 1-4 EEL = -2462.2275
> > VDWAALS = 11458.8455 EELEC = -96105.1590 EHBOND =
> > 0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL =
> > 34271.8077 VOLUME =
> > 231284.2068 Density
> > = 0.8729 Ewald error estimate:
> > 0.1272E-03 ------------------------------------------------------------
> ------------------Coordinate
> > resetting (SHAKE) cannot be accomplished,deviation is too largeNITER,
> NIT,
> > LL, I and J are : 0 2 38 117 118 Note: This is
> > usually a symptom of some deeper problem with the energetics of the
> > system.*
> >
> > When i had a look into the rst file of the previous minimization run, i
> > found that it cannot be opened or read.
> >
> > I have tried using the system on both versions of AMBER (10 and 16). The
> > same error persists.
> >
> > I am not getting a clue into how this can happen??
> >
> > Thanks in advance......
> >
> > Mr. Prayagraj Fandilolu
> > Research Scholar,
> > Structural Bioinformatics Unit
> > Department of Biochemistry
> > Shivaji University, Kolhapur - 416004
> > (MS) India
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Wed Oct 19 2016 - 03:30:02 PDT
