Re: [AMBER] format error from mmpbsa.py

From: Jason Swails <jason.swails.gmail.com>
Date: Sat, 11 Jun 2011 21:02:20 -0600

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
>



-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032



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Received on Sat Jun 11 2011 - 20:30:03 PDT
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