Hi Oliver,
It would appear as though prmtop files and mdcrd files are incompatible
(that's usually the case when you see a ********** in the temporary output
file).
Try visualizing all of the _MMPBSA_*.mdcrd files with the corresponding
prmtop to see which one is warped. Specifically look for a warped bond.
There may be a bond in one of your prmtop files between 2 atoms that should
*not* be bonded together (this would cause the bond term to blow up while
the others are OK).
HTH,
Jason
On Mon, May 16, 2011 at 10:22 PM, Oliver Kuhn <oak.amber.googlemail.com>wrote:
> MMPBSA calculation input file
> &general
> startframe=1, endframe=200, interval=1,
> verbose=2,
> strip_mask=:200-204:206-8051
> /
> &pb
> sander_apbs=1, indi=1,
> /
>
> receptor is 1-198
> ligand is 199
> water is 205
> last (water) residue is 8051
>
> Maximum number of minimization cycles reached.
>
> And the energy problem is not only for one but all snapshots:
>
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 1.3918E+08 6.0401E+04 1.8073E+05 C3 13
>
> BOND = ************* ANGLE = 8568.5539 DIHED =
> 324.6412
> VDWAALS = 1502.4033 EEL = 6.2939 EPB =
> -978.2764
> 1-4 VDW = -0.0005 1-4 EEL = -4.6667 RESTRAINT =
> 0.0000
> ENPOLAR = 40.9749
> minimization completed, ENE= 0.13917949E+09 RMS= 0.604013E+05
> minimizing coord set # 27
>
>
> Maximum number of minimization cycles reached.
>
>
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 1.5284E+08 6.1880E+04 1.9712E+05 O 71
>
> BOND = ************* ANGLE = 7841.0018 DIHED =
> 271.8407
> VDWAALS = -0.0418 EEL = -37.5258 EPB =
> -961.8115
> 1-4 VDW = -0.0027 1-4 EEL = 20.7267 RESTRAINT =
> 0.0000
> ENPOLAR = 41.0488
> minimization completed, ENE= 0.15284473E+09 RMS= 0.618804E+05
> minimizing coord set # 28
>
>
> Maximum number of minimization cycles reached.
>
>
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 1.4857E+08 6.3355E+04 2.1190E+05 C3 13
>
> BOND = ************* ANGLE = 9474.7097 DIHED =
> 297.6169
> VDWAALS = -0.0237 EEL = 0.0768 EPB =
> -986.7307
> 1-4 VDW = -0.0000 1-4 EEL = 0.9346 RESTRAINT =
> 0.0000
> ENPOLAR = 41.2883
> minimization completed, ENE= 0.14856890E+09 RMS= 0.633553E+05
> minimizing coord set # 29
>
>
> Maximum number of minimization cycles reached.
>
>
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 1.1970E+08 5.5393E+04 1.7757E+05 S1 7
>
> BOND = ************* ANGLE = 8193.2024 DIHED =
> 289.4883
> VDWAALS = -0.1859 EEL = -59.7277 EPB =
> -912.0416
> 1-4 VDW = -0.0007 1-4 EEL = -4.2525 RESTRAINT =
> 0.0000
> ENPOLAR = 40.8737
> minimization completed, ENE= 0.11969814E+09 RMS= 0.553932E+05
> minimizing coord set # 30
>
>
> Maximum number of minimization cycles reached.
>
>
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 1.5478E+08 6.6942E+04 2.3440E+05 C20 55
>
> BOND = ************* ANGLE = 10027.3003 DIHED =
> 265.0834
> VDWAALS = -0.0028 EEL = -5.4611 EPB =
> -974.1943
> 1-4 VDW = -0.0001 1-4 EEL = 4.8587 RESTRAINT =
> 0.0000
> ENPOLAR = 41.4313
> minimization completed, ENE= 0.15478438E+09 RMS= 0.669419E+05
> minimizing coord set # 31
>
>
>
>
> --
> Oliver Kuhn, Department of Bioinformatics,
> Center for Medical Biotechnology, University of Duisburg-Essen,
> Universitätsstr. 1-5, 45141 Essen, Germany
> phone +49 201 183-3121, oliver.kuhn.uni-due.de
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon May 16 2011 - 14:00:02 PDT
