Re: [AMBER] format error from mmpbsa.py

From: Jason Swails <jason.swails.gmail.com>
Date: Sat, 11 Jun 2011 16:57:27 -0600

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)
> 
> *****************************************************************
> 
> 
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Received on Sat Jun 11 2011 - 16:00:02 PDT