Hey, I have problem with MMPBSA.py. I am not sure if it is caused by my
topology files, which were generated with CHAMBER. Any suggestions how I
can solve this?
Cheers,
Zhi
******************ERROR INFO*****************************
/home/zw258/code/AMBER/amber11/AmberTools/bin/MMPBSA -i mmpbsa.in\
-o mmpbsa.out\
-sp /home/zw258/apelin_npt/mmpbsa/input/vmd_prmtop\
-cp /home/zw258/apelin_npt/mmpbsa/input/vmd-comp\
-rp /home/zw258/apelin_npt/mmpbsa/input/vmd-rec\
-lp /home/zw258/apelin_npt/mmpbsa/input/vmd-lig\
-y /home/zw258/apelin_npt/combined_18.crd
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
Traceback (most recent call last):
File
"/home/zw258/code/AMBER/amber11/AmberTools/src/mmpbsa_py/MMPBSA.py",
line 420, in <module>
solv_prm = amberParm(FILES['solvated_prmtop'])
File
"/home/zw258/code/AMBER/amber11/lib/python2.6/chemistry/amber/readparm.py",
line 164, in __init__
self.rdparm() # read the prmtop
File
"/home/zw258/code/AMBER/amber11/lib/python2.6/chemistry/amber/readparm.py",
line 278, in rdparm
number_items_perline, size_item, dat_type =
_parseFormat(self.formats[current_flag])
File
"/home/zw258/code/AMBER/amber11/lib/python2.6/chemistry/amber/readparm.py",
line 123, in _parseFormat
return int(format_parts[0]), int(format_parts[1]), 'str'
ValueError: invalid literal for int() with base 10: 'i2,'
make: *** [cal] Error 1
*******************************************************************
Makefile:
******************************
NAME=apelin_apj_popc
# Environment
AMBERHOME=/home/zw258/code/AMBER/amber11
MMPBSA=$(AMBERHOME)/AmberTools/bin/MMPBSA
MMPBSA_HOME=/home/zw258/apelin_npt/mmpbsa/input
SYS=$(MMPBSA_HOME)/vmd_prmtop
COMP=$(MMPBSA_HOME)/vmd-comp
REC=$(MMPBSA_HOME)/vmd-rec
LIG=$(MMPBSA_HOME)/vmd-lig
CRD=/home/zw258/apelin_npt/combined_18.crd
all: cal
cal: $(SYS) $(COMP) $(REC) $(LIG) $(CRD)
$(MMPBSA) -i mmpbsa.in\
-o mmpbsa.out\
-sp $(SYS)\
-cp $(COMP)\
-sp $(SYS)\
-cp $(COMP)\
-rp $(REC)\
-lp $(LIG)\
-y $(CRD)
*****************************************************************
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Received on Sat Jun 11 2011 - 14:30:03 PDT
