Dear Amber users,
I am running MMPBSA.py.MPI using the following command -
>mpirun -np 4 ~/src/Xtruct/trunk/amber_10_install/bin/MMPBSA.py.MPI -O -i
mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp solvated_complex.prmtop -cp
complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y *.mdcrd
Everytime (with zinc ions, without zn ions, with/without crystallographic
waters), I get the following error (this error occurs even when i run
MMPBSA.py with input files provided in tutorial 3.2) ---->
MMPBSA.py.MPI being run on 4 processors
ptraj found! Using /home/ksahu/src/Xtruct/trunk/amber_10_install/bin/ptraj
sander found! Using /home/ksahu/src/Xtruct/trunk/amber_10_install/bin/sander
Warning: igb=2 should be used with mbondi2 pbradii set. Yours are modified
Bondi radii (mbondi)
Preparing trajectories with ptraj...
21 frames were read in and processed by ptraj for use in calculation.
Starting calculations
Starting gb calculation...
calculating ligand contribution...
calculating receptor contribution...
calculating complex contribution...
Cannot match namelist object name ipb
namelist read: missplaced = sign
Cannot match namelist object name inp
namelist read: missplaced = sign
Cannot match namelist object name ipb
namelist read: missplaced = sign
Cannot match namelist object name inp
namelist read: missplaced = sign
Cannot match namelist object name ipb
namelist read: missplaced = sign
Cannot match namelist object name inp
namelist read: missplaced = sign
Cannot match namelist object name ipb
namelist read: missplaced = sign
Cannot match namelist object name inp
namelist read: missplaced = sign
Cannot match namelist object name ipb
namelist read: missplaced = sign
Cannot match namelist object name inp
namelist read: missplaced = sign
Cannot match namelist object name ipb
namelist read: missplaced = sign
Cannot match namelist object name inp
namelist read: missplaced = sign
Cannot match namelist object name ipb
namelist read: missplaced = sign
Cannot match namelist object name inp
namelist read: missplaced = sign
Cannot match namelist object name ipb
namelist read: missplaced = sign
Cannot match namelist object name inp
namelist read: missplaced = sign
Cannot match namelist object name ipb
namelist read: missplaced = sign
Cannot match namelist object name inp
namelist read: missplaced = sign
Starting pb calculation...
calculating ligand contribution...
Cannot match namelist object name ipb
namelist read: missplaced = sign
Cannot match namelist object name inp
namelist read: missplaced = sign
calculating receptor contribution...
Cannot match namelist object name ipb
namelist read: missplaced = sign
Cannot match namelist object name inp
namelist read: missplaced = sign
calculating complex contribution...
Cannot match namelist object name ipb
namelist read: missplaced = sign
Cannot match namelist object name inp
namelist read: missplaced = sign
Calculations complete. Writing output file(s)...
Error: No potential terms in sander output! Check output files.
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.
The FINAL_RESULTS_MMPBSA.dat file reads -
| Run on Fri Jul 2 10:22:39 JST 2010
|Input file:
|--------------------------------------------------------------
|Input file for running PB and GB
|&general
| endframe=50, verbose=1,
|# entropy=1,
|/
|&gb
| igb=2, saltcon=0.100,
| gbsa=1
|/
|&pb
| istrng=0.100,
|/
|--------------------------------------------------------------
|Complex topology file: complex.prmtop
|Receptor topology file: receptor.prmtop
|Ligand topology file: ligand.prmtop
|Initial mdcrd(s): equil.mdcrd
|
|Best guess for receptor mask: ":1-423:425-599"
|Best guess for ligand mask: ":424"
|Ligand residue name is "SAM"
|
|Calculations performed using 25 frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in
sander.
|
|All units are reported in kcal/mole.
Is this a prolem with installation or something ?
Thank you
Best Regards,
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Received on Sun Jul 04 2010 - 19:00:03 PDT
