On 2011-6-12 11:02, Jason Swails wrote:
> I think I fixed the problem. Put the attached file in
> $AMBERHOME/AmberTools/src/etc/chemistry/amber, and run the commands:
>
> cd $AMBERHOME/AmberTools/src/etc
> make install
>
> Then try it again. If this works, I'll post it as a bugfix on the amber
> website.
>
> Thanks!
> Jason
>
> On Sat, Jun 11, 2011 at 4:57 PM, Jason Swails<jason.swails.gmail.com>wrote:
>
>> It appears as though the topology file class doesn't work with chamber
>> topology files... I've never seen one of those topology files, and I didn't
>> know anything was that fundamentally different with them.
>>
>> I'll work on a patch.
>>
>> All the best,
>> Jason
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>>
>> On Jun 11, 2011, at 3:01 PM, Zhi Wang<zw258.cam.ac.uk> wrote:
>>
>>> 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)
>>>
>>> *****************************************************************
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
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> AMBER.ambermd.org
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It starts calculation but get another error when GB calculations begins.
***************ERROR INFO*********************************
Beginning GB calculations with mmpbsa_py_energy...
calculating complex contribution...
Error: mmpbsa_py_energy error during GB calculations!
NOTE: All files have been retained for debugging purposes. Type
MMPBSA.py --clean to erase these files.
make: *** [cal] Error 1
******************************************************************
Having a look at _MMPBSA_complex_gb.mdout file, it seems still the
problem with format of parm file.
*********************_MMPBSA_complex_gb.mdout********************
Reading parm file (/home/zw258/apelin_npt/mmpbsa/input/comp.prmtop)
Error: line too long in TITLE:
%FORMAT(10I8)
*******************************************************************************
Regards,
Zhi
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Received on Sun Jun 12 2011 - 02:30:03 PDT
