Hello,
I used igb=5 and igb=6 both, but these gave me too large number and
NaN error on output.
--------------------------------
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.7889E+21 1.5519E+22 4.7343E+23 CD 307
BOND = 6254035.9830 ANGLE = 72443.8361 DIHED = 1478.1915
VDWAALS = ************* EEL = -6022.1977 EGB = 0.0000
1-4 VDW = 9715179.9302 1-4 EEL = 836.5689 RESTRAINT = 0.0000
-bash-3.2$ tail 2hb2_equil_x_wat.out
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 NaN NaN 1.1769E+06 CG 145
BOND = ************* ANGLE = 69232.1399 DIHED = 1514.8657
VDWAALS = NaN EEL = +Infinity EGB = 0.0000
1-4 VDW = -0.0007 1-4 EEL = 104.8996 RESTRAINT = 0.0000
-bash-3.2$ tail 2hb2_equil_x_wat.out
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.2140E+08 8.3418E+05 1.1472E+07 OE2 364
BOND = ************* ANGLE = 65089.4218 DIHED = 1452.7606
VDWAALS = 5545981.4707 EEL = -1282.8808 EGB = 0.0000
1-4 VDW = 533470.1871 1-4 EEL = 891.5496 RESTRAINT = 0.0000
--------------------------------------------------------
I guess it looks like there are some bugs when ptraj extracted coordinates.
Quoting Jason Swails <jason.swails.gmail.com>:
> It sounds like it's still trying to use the box information, which it really
> shouldn't if you've stripped the waters. Do you want to run in some kind of
> GB or PB implicit solvent, or just vacuum (gas phase) energies?
>
> Try setting the igb variable to the GB model you want to use (or set it to 6
> if you want vacuum). Does this fix your problem?
>
> Good luck,
> Jason
>
> On Wed, Dec 1, 2010 at 2:49 PM, Bongkeun Kim <bkim.chem.ucsb.edu> wrote:
>
>> Hello,
>>
>> I extracted peptide only mdcrd from the explicit water simulation with
>> the peptide only prmtop file.
>> And I tried to calculate EPTOT for the peptide with the following input.
>> =================================
>> extract energy
>> &cntrl
>> imin = 5,
>> maxcyc = 1,
>> ntpr=1, ntwx=1,
>> ntb=0, cut=999
>> /
>> =================================
>>
>> Error occurs after few steps of calculations like:
>> ---------------------------------------------
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 1 1.3554E+02 1.8784E+01 8.2938E+01 CG 85
>>
>> BOND = 130.6848 ANGLE = 379.7738 DIHED =
>> 352.5286
>> VDWAALS = -124.5685 EEL = -2520.8371 HBOND =
>> 0.0000
>> 1-4 VDW = 132.3825 1-4 EEL = 1785.5740 RESTRAINT =
>> 0.0000
>> minimization completed, ENE= 0.13553800E+03 RMS= 0.187837E+02
>> minimizing coord set # 2
>> Frac coord min, max: 0.168166141059582 1.09509660191633
>> The system has extended beyond
>> the extent of the virtual box.
>> Restarting sander will recalculate
>> a new virtual box with 30 Angstroms
>> extra on each side, if there is a
>> restart file for this configuration.
>> SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
>> Atom out of bounds. If a restart has been written,
>> restarting should resolve the error
>> --------------------------------------------------------
>>
>>
>> I checked mdcrd file and found too large number of coordinates with
>> less precision.
>> ---------------------------------------
>> 1.000 2.000 0.000 3.000 9.000 3.000 4.000 8.000
>> 9.000 1.000
>> 1.000 8.000 3.000 5.000 3.000 9.000 5.000 1.000
>> 0.000 4.000
>> 5.000 3.000 2.000 9.000 3.000 1.000 3.000 5.000
>> 2.000 7.000
>> 6.000 6.000 6.000 2.000 8.000 2.000 8.000 0.000
>> 7.000 3.000
>> 0.000 3.000 8.000 8.000 2.000 7.000 4.000 5.000
>> 6.000 2.000
>> 0.000 0.000 2.000 4.000 2.000 6.000 5.000 0.000
>> 3.000 4.000
>> 9.000 3.000 6.000 4.000 1.000 4.000 5.000 0.000
>> 1.000 6.000
>> 2.000 7.000 8.000 5.000 4.000 3.000 6.000 1.000
>> 1.000 9.000
>> 6.000 3.000 9.000 6.000 1.000 5.000 1.000 8.000
>> 0.000 8.000
>> 7.000 8.000 3.000 5.000 7.000 8.000 6.000 7.000
>> 8.000 7.000
>> 7.000 1.000 4.000 7.000 9.000 1.000 0.000 8.000
>> 9.000 0.000
>> 7.000 4.000 3.000 2.000 4.000 2.000 8.000 1.000
>> 7.000 9.000
>> 5.000 8.000 0.000 0.000 6.000 9.000 1.000 9.000
>> 1.000 9.000
>> 7.000 4.000 8.000 2.000 1.000 1.000 2.000 4.000
>> 4.000 0.000
>> 0.000 6.000 6.000 8.000 6.000 6.000 9.000 4.000
>> 1.000 3.000
>> 8.000 8.000 0.000 6.000 5.000 1.000 1.000 0.000
>> 8.000 9.000
>> 1.000 2.000 8.000 7.000 7.000 7.000 1.000 5.000
>> 0.000 8.000
>> 5.000 2.000 3.000 7.000 0.000 3.000 2.000 7.000
>> 3.000 9.000
>> 7.000 8.000 9.000 0.000 5.000 1.000 7.000 2.000
>> 9.000 1.000
>> 9.000 7.000 0.000 2.000 1.000 2.000 1.000 9.000
>> 41.088 9.420 62.665 41.721 9.148 61.455 41.567 10.044
>> 35.604 26.216
>> 21.505 34.680 26.278 21.261 35.621 26.433 22.437 14.278
>> 11.771 31.180
>> 13.541 12.366 31.319 14.961 12.321 30.796 16.130 29.593
>> 25.338 15.722
>> 30.307 25.829 15.438 29.277 24.757 16.856 41.297 2.102
>> 17.512 40.872
>> 2.655 16.070 41.333 2.647 36.490 3.145 5.092 36.652
>> 4.079 5.219
>> 37.363 2.759 5.015 7.146 2.097 0.247 7.539 1.234
>> 0.117 7.889
>> 2.701 0.249 48.336 17.814 3.189 48.102 16.902 3.019
>> 49.070 17.762
>> 3.801 35.401 29.453 25.979 34.841 30.226 25.920 36.101
>> 29.615 25.346
>> --------------------------------------------------------------
>>
>> I'm using AMBER 11 GPU with the recent bugfix 12.
>> If you have any idea, please let me know.
>> Thank you.
>> Bongkeun Kim
>>
>>
>>
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>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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>
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Received on Wed Dec 01 2010 - 13:00:04 PST
