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
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Received on Fri Sep 18 2009 - 03:30:02 PDT
