Ah, it appears as though nab cannot handle a chamber-created topology file,
which makes sense. The CHARMM-specific potential terms are not coded into
nab.
To fix this, you *must* have Amber11, and put the variable "use_sander=1" in
your MMPBSA.py input file.
Does this work?
All the best,
Jason
On Sun, Jun 12, 2011 at 3:02 AM, Zhi Wang <zw258.cam.ac.uk> wrote:
> 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
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> 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
> _______________________________________________
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jun 12 2011 - 10:00:02 PDT
