Dear Amber experts,
Last time I post my question into the forum asking why
my protein jump out. Thank some people advice me that
I can use ptraj to put the image of my protein back.
This is maybe normal and acceptable if the protein
moving out slowly, as you advice it’s just an image in
periodic system.
However, my supervisor wonders something must be wrong
because my protein jump out at the first time step of
simulation and both EP and EK increase suddenly.
Time step 0: EK=0 EP=-240528
Temp=0
1: EK=27062 EP=-240528
Temp=223.11
2: EK=22866 EP=-209771
Temp=188.52
3: EK=13.9
EP=-209782 Temp=0.11
I don’t know what I’ve done wrong? How can I control
the energy at the first step??? Please help.
Sorry if my email is too long.
I greatly appreciate any of you advice.
Best wishes,
Lich Nguyen
Following is my input and output of the first few step
I use Amber7 and force field 99.
After minimization, my protein is well surrounded by
water. I continued to heat up my system to 305K.
This is the output:
-------------------------------------------------------
Amber 7 SANDER
Scripps/UCSF 2002
-------------------------------------------------------
| Thu Nov 21 10:59:05 2002
[-O]verwriting output
File Assignments:
| MDIN: heat_short.in
| MDOUT: heat_takalong_32.out
|INPCRD: taka_min.xyz
| PARM: taka.parm
|RESTRT: heat_takalong_32.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: heat_takalong_32.crd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
# heating of Taka amylase with temperature ramp to
32oC
&cntrl
imin=0, nmropt=1
nstlim=10000, dt=0.001,
ntpr=1, ntwr=1000, iwrap=1, ntwx=1,
ntf=2, ntc=2, ntb=1,
ntt=1,
&end
&wt type='TEMP0', istep1=0,istep2=1000,value1=0.0,
value2=5.0, &end
&wt type='TEMP0', istep1=1001,istep2=5000,value1=5.0,
value2=100.0, &end
&wt type='TEMP0',
istep1=5001,istep2=10000,value1=100.0,
value2=305.0, &end
&wt type='TAUTP', istep1=0,istep2=5000,value1=0.5,
value2=0.5, &end
&wt type='TAUTP',
istep1=5001,istep2=10000,value1=0.5,
value2=0.1, &end
&wt type='END' &end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
| New format PARM file being parsed.
| Version = 1.000 Date = 11/19/02 Time = 15:18:38
NATOM = 59188 NTYPES = 18 NBONH = 55485
MBONA = 3786
NTHETH = 7894 MTHETA = 5174 NPHIH = 15156
MPHIA = 9586
NHPARM = 0 NPARM = 0 NNB = 108918
NRES = 17825
NBONA = 3786 NTHETA = 5174 NPHIA = 9586
NUMBND = 43
NUMANG = 90 NPTRA = 41 NATYP = 31
NPHB = 1
IFBOX = 2 NMXRS = 24 IFCAP = 0
NEXTRA = 0
| Memory Use Allocated Used
| Real 16000000 3896925
| Hollerith 4000000 372955
| Integer 8000000 4131254
| Max Nonbonded Pairs:15000000
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: TRUNCATED OCTAHEDRON
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 0, nmropt = 1
Nature and format of input:
ntx = 1, irest = 0, ntrx =
1
Nature and format of output:
ntxo = 1, ntpr = 1, ntrx =
1, ntwr = 1000
iwrap = 1, ntwx = 1, ntwv =
0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp =
0, rbornstat= 0
Potential function:
ntf = 2, ntb = 1, igb =
0, nsnb = 25
ipol = 0, gbsa = 0
dielc = 1.00000, cut = 8.00000, intdiel
= 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 10000, nscm = 1000, nrespa =
1
t = 0.00000, dt = 0.00100, vlimit
= 20.00000
Temperature regulation:
ig = 71277, ntt = 1, vrand =
0
temp0 = 300.00000, tempi = 0.00000, heat
= 0.00000
dtemp = 5.00000, tautp = 1.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
NMR refinement options:
iscale = 0, noeskp = 1, ipnlty =
1, mxcub = 1
scalm = 100.00000, pencut = 0.10000, tausw
= 0.10000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag =
1, use_pme = 1
vdwmeth = 1, eedmeth = 1, frc_int =
0, netfrc = 1
Box X = 95.121 Box Y = 95.121 Box Z =
95.121
Alpha = 109.471 Beta = 109.471 Gamma =
109.471
NFFT1 = 96 NFFT2 = 96 NFFT3 =
96
Cutoff= 8.000 Tol =0.100E-04
Ewald Coefficient = 0.34864
Interpolation order = 4
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Begin reading energy term weight
changes/NMR restraints
WEIGHT CHANGES:
TEMP0 0 1000 0.000000 5.000000 0
0
TEMP0 1001 5000 5.000000 100.000000 0
0
TEMP0 5001 10000 100.000000 305.000000 0
0
TAUTP 0 5000 0.500000 0.500000 0
0
TAUTP 5001 10000 0.500000 0.100000 0
0
RESTRAINTS:
** No restraint defined **
Done reading weight changes/NMR
restraints
Number of triangulated 3-point waters found: 17333
Sum of charges from parm topology file =
-0.00000032
Forcing neutrality...
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC
SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to
cutoff
| CHECK switch(x): max rel err = 0.3242E-14 at
2.436720
| CHECK d/dx switch(x): max rel err = 0.8156E-11
at 2.782960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 11064090
| TOTAL SIZE OF NONBOND LIST = 11064090
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) =
0.00 PRESS = 0.0
Etot = -240528.7770 EKtot = 0.0000 EPtot
= -240528.7770
BOND = 229.6517 ANGLE = 929.7232 DIHED
= 4021.7227
1-4 NB = 1531.6713 1-4 EEL = 22462.9588
VDWAALS = 31972.1640
EELEC = -301676.6686 EHBOND = 0.0000
RESTRAINT = 0.0000
Ewald error estimate: 0.2613E-03
------------------------------------------------------------------------------
===============================================================================
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
===============================================================================
NSTEP = 1 TIME(PS) = 0.001 TEMP(K) =
223.11 PRESS = 0.0
Etot = -213466.6893 EKtot = 27062.0877 EPtot
= -240528.7770
BOND = 229.6517 ANGLE = 929.7232 DIHED
= 4021.7227
1-4 NB = 1531.6713 1-4 EEL = 22462.9588
VDWAALS = 31972.1640
EELEC = -301676.6686 EHBOND = 0.0000
RESTRAINT = 0.0000
Ewald error estimate: 0.2613E-03
------------------------------------------------------------------------------
===============================================================================
NMR restraints for step 1
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
===============================================================================
NSTEP = 2 TIME(PS) = 0.002 TEMP(K) =
188.52 PRESS = 0.0
Etot = -186904.9198 EKtot = 22866.9251 EPtot
= -209771.8449
BOND = 230.4107 ANGLE = 927.4944 DIHED
= 4021.5139
1-4 NB = 1531.5068 1-4 EEL = 22463.3568
VDWAALS = 32049.2707
EELEC = -270995.3982 EHBOND = 0.0000
RESTRAINT = 0.0000
Ewald error estimate: 0.2616E-03
------------------------------------------------------------------------------
===============================================================================
NMR restraints for step 2
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
===============================================================================
NSTEP = 3 TIME(PS) = 0.003 TEMP(K) =
0.11 PRESS = 0.0
Etot = -209768.9615 EKtot = 13.9125 EPtot
= -209782.8740
BOND = 229.6823 ANGLE = 924.6021 DIHED
= 4021.3978
1-4 NB = 1531.4638 1-4 EEL = 22463.3250
VDWAALS = 32044.3100
EELEC = -270997.6549 EHBOND = 0.0000
RESTRAINT = 0.0000
Ewald error estimate: 0.2619E-03
------------------------------------------------------------------------------
===============================================================================
NMR restraints for step 3
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
===============================================================================
NSTEP = 4 TIME(PS) = 0.004 TEMP(K) =
0.26 PRESS = 0.0
Etot = -209769.1788 EKtot = 31.9512 EPtot
= -209801.1300
BOND = 228.7016 ANGLE = 920.5913 DIHED
= 4021.2228
1-4 NB = 1531.4036 1-4 EEL = 22463.2699
VDWAALS = 32034.6354
EELEC = -271000.9546 EHBOND = 0.0000
RESTRAINT = 0.0000
Ewald error estimate: 0.2646E-03
------------------------------------------------------------------------------
===============================================================================
NMR restraints for step 4
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
===============================================================================
NSTEP = 5 TIME(PS) = 0.005 TEMP(K) =
0.46 PRESS = 0.0
Etot = -209769.4254 EKtot = 55.1974 EPtot
= -209824.6227
BOND = 227.7429 ANGLE = 916.4053 DIHED
= 4021.0123
1-4 NB = 1531.3369 1-4 EEL = 22463.1910
VDWAALS = 32020.3033
EELEC = -271004.6144 EHBOND = 0.0000
RESTRAINT = 0.0000
Ewald error estimate: 0.2668E-03
------------------------------------------------------------------------------
===============================================================================
NMR restraints for step 5
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
===============================================================================
NSTEP = 6 TIME(PS) = 0.006 TEMP(K) =
0.67 PRESS = 0.0
Etot = -209769.7139 EKtot = 81.5955 EPtot
= -209851.3094
BOND = 227.0310 ANGLE = 912.9449 DIHED
= 4020.7924
1-4 NB = 1531.2750 1-4 EEL = 22463.0879
VDWAALS = 32001.3494
EELEC = -271007.7900 EHBOND = 0.0000
RESTRAINT = 0.0000
Ewald error estimate: 0.2689E-03
------------------------------------------------------------------------------
===============================================================================
NMR restraints for step 6
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
===============================================================================
NSTEP = 7 TIME(PS) = 0.007 TEMP(K) =
0.90 PRESS = 0.0
Etot = -209770.0246 EKtot = 109.3520 EPtot
= -209879.3766
BOND = 226.6649 ANGLE = 910.8212 DIHED
= 4020.5882
1-4 NB = 1531.2244 1-4 EEL = 22462.9626
VDWAALS = 31977.8304
EELEC = -271009.4684 EHBOND = 0.0000
RESTRAINT = 0.0000
Ewald error estimate: 0.2700E-03
------------------------------------------------------------------------------
===============================================================================
NMR restraints for step 7
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
===============================================================================
NSTEP = 8 TIME(PS) = 0.008 TEMP(K) =
1.13 PRESS = 0.0
Etot = -209770.3978 EKtot = 137.1833 EPtot
= -209907.5811
BOND = 226.5988 ANGLE = 910.2108 DIHED
= 4020.4200
1-4 NB = 1531.1853 1-4 EEL = 22462.8198
VDWAALS = 31949.8302
EELEC = -271008.6461 EHBOND = 0.0000
RESTRAINT = 0.0000
Ewald error estimate: 0.2743E-03
------------------------------------------------------------------------------
===============================================================================
NMR restraints for step 8
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
===============================================================================
NSTEP = 9 TIME(PS) = 0.009 TEMP(K) =
1.36 PRESS = 0.0
Etot = -209770.7640 EKtot = 164.3592 EPtot
= -209935.1232
BOND = 226.6863 ANGLE = 910.8532 DIHED
= 4020.3015
1-4 NB = 1531.1516 1-4 EEL = 22462.6650
VDWAALS = 31917.3977
EELEC = -271004.1785 EHBOND = 0.0000
RESTRAINT = 0.0000
Ewald error estimate: 0.2763E-03
------------------------------------------------------------------------------
===============================================================================
NMR restraints for step 9
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
===============================================================================
NSTEP = 10 TIME(PS) = 0.010 TEMP(K) =
1.57 PRESS = 0.0
Etot = -209771.1725 EKtot = 190.5668 EPtot
= -209961.7393
BOND = 226.7638 ANGLE = 912.1820 DIHED
= 4020.2389
1-4 NB = 1531.1125 1-4 EEL = 22462.5042
VDWAALS = 31880.5545
EELEC = -270995.0952 EHBOND = 0.0000
RESTRAINT = 0.0000
Ewald error estimate: 0.2763E-03
------------------------------------------------------------------------------
===============================================================================
NMR restraints for step 10
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
===============================================================================
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Received on Tue Nov 26 2002 - 23:42:29 PST
