See the reason behind this erroris unallocation of memory space.
Better increase the memory size of stack to run this.
If you are windows user, increase virtual memory. Or if you are using
linux, increase the stacksize.
You may also remove trivial parameters from the run, to decrease the
allocated memory requirement.
On 9/18/09, Jio M <jiomm.yahoo.com> wrote:
> Dear Amber users;
>
>
>
> I have ligand protein complex with waterbox.. I did minimisation with SHAKE
> then this LINMIN failure came...
>
>
>
> but it was suggested to do first minimisation without SHAKE then second
> minimisation with SHAKE..in this case I got no error in first
> minimisation but with SHAKE LINMIN failure again noticed.. what
> is reason and solution for this .......
>
>
>
> min_noSHAKE.in
>
>
>
>
>
> &cntrl
>
> imin=1,maxcyc=1000,ncyc=500,
>
> cut=8.0,ntb=1,
>
> ntc=1,ntf=1,
>
> ntpr=100,
>
> ntr=1, restraintmask=':207-478',
>
> restraint_wt=2.0
>
> /
>
>
>
> min.in file
>
>
>
> &cntrl
>
> imin=1,maxcyc=1000,ncyc=500,
>
> cut=8.0,ntb=1,
>
> ntc=2,ntf=2,
>
> ntpr=100,
>
> ntr=1, restraintmask=':207-478',
>
> restraint_wt=2.0
>
> /
>
>
>
> 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 = 0.2738E-14 at 2.422500
>
> | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
>
> ---------------------------------------------------
>
> | Local SIZE OF NONBOND LIST = 507119
>
> | TOTAL SIZE OF NONBOND LIST = 7982221
>
>
>
>
>
> NSTEP
> ENERGY
> RMS
> GMAX
> NAME NUMBER
>
> 1
> -1.5371E+05 1.8408E+01
> 6.1403E+01
> O 9015
>
>
>
> BOND =
> 139.7029 ANGLE =
> 585.9775 DIHED
> = 2697.3324
>
> VDWAALS = 26288.8749
> EEL = -196992.8151
> HBOND
> = 0.0000
>
> 1-4 VDW = 935.1457 1-4 EEL
> = 12636.5467 RESTRAINT
> = 1.3255
>
> EAMBER = -153709.2350
>
>
>
>
>
> NSTEP
> ENERGY
> RMS
> GMAX
> NAME NUMBER
>
> 100
> -1.5371E+05 1.8408E+01
> 6.1382E+01
> O 9015
>
>
>
> BOND =
> 139.6206 ANGLE =
> 585.9935 DIHED
> = 2697.3411
>
> VDWAALS = 26285.6160
> EEL = -196988.8291
> HBOND
> = 0.0000
>
> 1-4 VDW = 935.1360 1-4 EEL
> = 12636.5486 RESTRAINT
> = 1.3329
>
> EAMBER = -153708.5731
>
>
>
>
>
> NSTEP
> ENERGY
> RMS
> GMAX
> NAME NUMBER
>
> 200
> -1.5371E+05 1.8408E+01
> 6.1382E+01
> O 9015
>
>
>
> BOND =
> 139.6198 ANGLE =
> 585.9938 DIHED
> = 2697.3412
>
> VDWAALS = 26285.5845
> EEL = -196988.7917
> HBOND
> = 0.0000
>
> 1-4 VDW = 935.1359 1-4 EEL
> = 12636.5488 RESTRAINT
> = 1.3330
>
> EAMBER = -153708.5677
>
>
>
>
>
> NSTEP
> ENERGY
> RMS
> GMAX
> NAME NUMBER
>
> 300
> -1.5371E+05 1.8408E+01
> 6.1382E+01
> O 9015
>
>
>
> BOND =
> 139.6190 ANGLE =
> 585.9939 DIHED
> = 2697.3413
>
> VDWAALS = 26285.5526
> EEL = -196988.7510
> HBOND
> = 0.0000
>
> 1-4 VDW = 935.1358 1-4 EEL
> = 12636.5484 RESTRAINT
> = 1.3331
>
> EAMBER = -153708.5599
>
>
>
>
>
> NSTEP
> ENERGY
> RMS
> GMAX
> NAME NUMBER
>
> 400
> -1.5371E+05 1.8408E+01
> 6.1382E+01
> O 9015
>
>
>
> BOND =
> 139.6181 ANGLE =
> 585.9941 DIHED
> = 2697.3414
>
> VDWAALS = 26285.5202
> EEL = -196988.7128
> HBOND
> = 0.0000
>
> 1-4 VDW = 935.1358 1-4 EEL
> = 12636.5483 RESTRAINT
> = 1.3331
>
> EAMBER = -153708.5548
>
>
>
>
>
> NSTEP
> ENERGY
> RMS
> GMAX
> NAME NUMBER
>
> 500
> -1.5371E+05 1.8408E+01
> 6.1382E+01
> O 9015
>
>
>
> BOND =
> 139.6174 ANGLE =
> 585.9943 DIHED
> = 2697.3415
>
> VDWAALS = 26285.4885
> EEL = -196988.6745
> HBOND
> = 0.0000
>
> 1-4 VDW = 935.1357 1-4 EEL
> = 12636.5485 RESTRAINT
> = 1.3332
>
> EAMBER = -153708.5486
>
>
>
> .... RESTARTED DUE TO LINMIN FAILURE ...
>
>
>
> .... RESTARTED DUE TO LINMIN FAILURE ...
>
>
>
> .... RESTARTED DUE TO LINMIN FAILURE ...
>
>
>
> .... RESTARTED DUE TO LINMIN FAILURE ...
>
>
>
>
>
> NSTEP
> ENERGY
> RMS
> GMAX
> NAME NUMBER
>
> 600
> -1.5371E+05 1.8408E+01
> 6.1382E+01
> O 9015
>
>
>
> BOND =
> 139.6171 ANGLE =
> 585.9943 DIHED
> = 2697.3415
>
> VDWAALS = 26285.4794
> EEL = -196988.6632
> HBOND
> = 0.0000
>
> 1-4 VDW = 935.1357 1-4 EEL
> = 12636.5486 RESTRAINT
> = 1.3332
>
> EAMBER = -153708.5465
>
>
>
> .... RESTARTED DUE TO LINMIN FAILURE ...
>
>
>
> ***** REPEATED LINMIN FAILURE *****
>
>
>
> ***** SEE http://amber.scripps.edu/Questions/linmin.html FOR MORE INFO
> *****
>
>
>
>
>
> FINAL RESULTS
>
>
>
>
>
>
>
> NSTEP
> ENERGY
> RMS
> GMAX
> NAME NUMBER
>
> 614
> -1.5371E+05 1.8408E+01
> 6.1382E+01
> O 9015
>
>
>
> BOND =
> 139.6171 ANGLE =
> 585.9943 DIHED
> = 2697.3415
>
> VDWAALS = 26285.4781
> EEL = -196988.6617
> HBOND
> = 0.0000
>
> 1-4 VDW = 935.1357 1-4 EEL
> = 12636.5486 RESTRAINT
> = 1.3332
>
> EAMBER = -153708.5463
>
>
>
> thanks:
>
> Jiomm
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Ashish Runthala,
Faculty Division III,
Assistant Lecturer, Biological Sciences,
Birla Institute of Technology and Science,
Pilani, Rajasthan- 333031
INDIA
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Received on Fri Sep 18 2009 - 04:00:01 PDT
