Hi,
Do you have ptraj/AmberTools patched up to the latest bugfix?
http://ambermd.org/bugfixesat.html
-Dan
On Wed, Dec 1, 2010 at 4:18 PM, Bongkeun Kim <bkim.chem.ucsb.edu> wrote:
> I made a pdb file which has peptide only from the last rst file.
> And I used it to the leap to generate prmtop and inpcrd files.
>
> In ptraj, my command is
> ptraj 2hb_xw.prmtop <extw.traj
> And in the extw.traj
> ----------
> trajin 2hb2_equil_wat4.mdcrd.gz 1 10000
> trajout 2hb2_equil_x_wat.mdcrd nobox
> --------------
>
> I used VMD to see the coordinates but it showed only crashed structure.
> Thank you for it.
> Bongkeun Kim
>
>
> Quoting Jason Swails <jason.swails.gmail.com>:
>
>> Try visualizing the trajectory with your favorite program (like VMD or
>> something) and see if you can see any obvious clashes.
>>
>> Also, did you specify "nobox" in your trajout statement when using ptraj?
>>
>> Good luck!
>> Jason
>>
>> On Wed, Dec 1, 2010 at 3:47 PM, Bongkeun Kim <bkim.chem.ucsb.edu> wrote:
>>
>>> 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
>>> >>
>>> >>
>>> >>
>>> >> _______________________________________________
>>> >> AMBER mailing list
>>> >> AMBER.ambermd.org
>>> >> http://lists.ambermd.org/mailman/listinfo/amber
>>> >>
>>> >
>>> >
>>> >
>>> > --
>>> > Jason M. Swails
>>> > Quantum Theory Project,
>>> > University of Florida
>>> > Ph.D. Graduate Student
>>> > 352-392-4032
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>> >
>>>
>>>
>>>
>>>
>>>
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>>>
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
>
>
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Received on Thu Dec 02 2010 - 12:00:03 PST
