Dear Dr. Nam,
Try checking the minimized starting structure (i.e. pre-dynamics). The
asterisks show that the potential energy is extremely high, so my guess is
that something is still wrong with the minimized conformation. Did the
minimization converge, and if so to what energy? In the min. output file
are listed the energy, the RMS gradient, and the maximum force with the
atom experiencing that force, so checking these listings may show a
persistent bad atomic contact of some kind.
Good luck--I hope this helps.
Sincerely,
Michael G. Cooney
Department of Biochemistry and Molecular Biology
The University of Georgia
Athens, GA 30602 USA
On Thu, 8 Mar 2001 kiyean.nam_at_pharma.Novartis.com wrote:
> Dear All,
>
> I have used sander in AMBER5.0 for MD simulation of 200aa protein.
> After relaxing the protein by series of minimization with several different
> force constants, I tried to equilibrate the system as shown in the
> following input file. But I got error message shown bottom of this message
> that I can not figure out what went wrong.
>
> Can anyone figure out what went wrong?
>
> Thank you.
>
> Kiyean Nam
>
> molecular dynamics equilibration run using PME
> &cntrl
> imin=0, ntc=2, ntf=2,
> init=3, ntx=1, irest=0,scee=1.2, ntr=0,
> ntb=2, ntp=1, npscal=1, pres0=1.0, taup=0.2,
> nrun=1, nstlim=20000, dt=0.002,
> temp0=300.0, tempI=0.0, ig=71277, ntt=5,
> nmropt=1, iewald=1, ntwx=500,
> &end
> 75.8453196 67.3903038 73.8507727 90.0000000 90.0000000 90.0000000
> 80 72 75 4 0 0 0
> 0.00001
> &wt
> type='TEMP0', istep1=0, istep2=2500,
> value1=0.0, value2=100.0,
> &end
> &wt
> type='TEMP0', istep1=2500, istep2=5000,
> value1=100.0, value2=200.0,
> &end
> &wt
> type='TEMP0', istep1=5000, istep2=7500,
> value1=200.0, value2=300.0,
> &end
> &wt
> type='TEMP0', istep1=7500, istep2=20000,
> value1=300.0, value2=300.0,
> &end
> &wt
> type='END',
> &end
> &rst
> iat=0,
> &end
>
>
> Error in output
>
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =**********
> Etot = ************ EKtot = 0.0000 EPtot = ************
> BOND = 126.9038 ANGLE = 607.6000 DIHED = 1044.2706
> 1-4 NB = 790.9668 1-4 EEL = 10119.1660 VDWAALS = ************
> EELEC = -178932.6354 EHBOND = 0.0000 CONSTRAINT = 0.0000
> EKCMT = 0.0000 VIRIAL = ************ VOLUME = 377468.9592
> T_SOLUTE = 0.0000 T_SOLVENT = 0.0000
> Density = 0.9774
> Ewald error estimate: 0.8941E-04
>
> ------------------------------------------------------------------------------
>
> ===============================================================================
> NMR restraints for step 0
> Energy (this step): Bond = 0.000 Angle = 0.000 Torsion =
> 0.000
> Energy (tot. run) : Bond = 0.000 Angle = 0.000 Torsion =
> 0.000
>
> DEVIATIONS: Target=(r2+r3)/2 Target = closer of r2/r3
> This step Entire run This step Entire run
> ave. rms ave. rms ave. rms ave.
> rms
> Bond 0.000 0.000 0.000 0.000 0.000 0.000 0.000
> 0.000
> Angle 0.000 0.000 0.000 0.000 0.000 0.000 0.000
> 0.000
> Torsion 0.000 0.000 0.000 0.000 0.000 0.000 0.000
> 0.000
> ===============================================================================
>
> COORDINATE RESETTING (SHAKE) WAS NOT ACCOMPLISHED
> WITHIN 3000 ITERATIONS
>
> .
> .
> .
> FATAL ERROR
>
Received on Thu Mar 08 2001 - 09:39:51 PST
