Hello,
using the serial version of MMPBSA.py i got the following error.
ptraj found! Using
/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/ptraj
sander found! Using
/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander
ptraj found! Using
/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/ptraj
sander found! Using
/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander
ptraj found! Using
/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/ptraj
sander found! Using
/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander
ptraj found! Using
/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/ptraj
sander found! Using
/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander
ptraj found! Using
/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/ptraj
ptraj found! Using
/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/ptraj
ptraj found! Using
/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/ptraj
sander found! Using
/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander
sander found! Using
/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander
sander found! Using
/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sandersander found!
Using /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander
Preparing trajectories with ptraj...
Preparing trajectories with ptraj...
Preparing trajectories with ptraj...
Preparing trajectories with ptraj...
Preparing trajectories with ptraj...
Preparing trajectories with ptraj...
Preparing trajectories with ptraj...mv: `_MMPBSA_dummycomplex.inpcrd.1' and
`_MMPBSA_dummycomplex.inpcrd' are the same file
mv: cannot stat `_MMPBSA_dummyreceptor.inpcrd.1': No such file or
directory300 frames were read in and processed by ptraj for use in
calculation.
Starting calculations...
Starting gb calculation...
calculating ligand contribution...
mv: cannot stat `_MMPBSA_dummyligand.inpcrd.1': No such file or directory
300 frames were read in and processed by ptraj for use in calculation.
Starting calculations...
Starting gb calculation...
calculating ligand contribution...
300 frames were read in and processed by ptraj for use in calculation.
calculating ligand contribution...
Error! Ptraj failed. Check coordinate and topology files for the
complex.NOTE: All files have been retained for debugging purposes. Type
MMPBSA.py --clean to erase these files.Error! Ptraj failed. Check coordinate
and topology files for the complex.300 frames were read in and processed by
ptraj for use in calculation.
Starting calculations...
Starting gb calculation...
calculating ligand contribution...
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.
Error! Ptraj failed. Check coordinate and topology files for the
complex.NOTE: All files have been retained for debugging purposes. Type
MMPBSA.py --clean to erase these files.
Error! Ptraj failed. Check coordinate and topology files for the
complex.NOTE: All files have been retained for debugging purposes. Type
MMPBSA.py --clean to erase these files.
calculating receptor contribution...
calculating receptor contribution...
calculating receptor contribution...
calculating receptor contribution... calculating complex contribution...
calculating complex contribution... calculating complex contribution...
calculating complex contribution...
Starting pb calculation...
calculating ligand contribution...
Starting pb calculation...
calculating ligand contribution...
Starting pb calculation...
calculating ligand contribution...
Starting pb calculation...
calculating ligand contribution...
calculating receptor contribution...
calculating receptor contribution...
calculating complex contribution...
Calculations complete. Writing output file(s)...
Error: Sander output is missing values!
VDWAALS = ************* EEL = -5060.4993 EGB =
-14223.5294NOTE: All files have been retained for debugging purposes. Type
MMPBSA.py --clean to erase these files.
calculating receptor contribution...
calculating receptor contribution...
calculating complex contribution...
calculating complex contribution...
calculating complex contribution...
Calculations complete. Writing output file(s)...
Error: Sander output is missing values!
VDWAALS = ************* EEL = -5060.4993 EGB =
-14223.5294NOTE: All files have been retained for debugging purposes. Type
MMPBSA.py --clean to erase these files.
Calculations complete. Writing output file(s)...
Error: Sander output is missing values!
VDWAALS = ************* EEL = -5060.4993 EGB =
-14223.5294NOTE: All files have been retained for debugging purposes. Type
MMPBSA.py --clean to erase these files.
Calculations complete. Writing output file(s)...
Error: Sander output is missing values!
VDWAALS = ************* EEL = -5060.4993 EGB =
-14223.5294NOTE: All files have been retained for debugging purposes. Type
MMPBSA.py --clean to erase these files.
Can anyone suggest me a solution to this.
Regards,
Vani
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Received on Sun Apr 10 2011 - 18:30:02 PDT
