Hi Joseph,
We were able to reproduce the error you described in your previous email
and are currently working on a patch. Thanks for your report.
2011/4/26 Joseph André <joseph.andre.ens.univ-evry.fr>
> Dear AmberTools users and developers,
> I'm new to AmberTools and MMPBSA. I was following MMPSA tutorials,
> section 3.3 on alanine scanning and I've got the following error when
> I try to compute binding energy calculation:
>
> $AMBERHOME/bin/MMPBSA -O -i mmpbsa_3.in -sp ras-raf_solvated.prmtop
> -cp ras-raf.prmtop -rp ras.prmtop -lp raf.prmtop -y *.mdcrd -mc
> rasraf_mutant.prmtop -mr ras_mutant.prmtop
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> ptraj found! Using /home/joseph/Logiciels/amber11-at1.5/bin/ptraj
> mmpbsa_py_energy found! Using
> /home/joseph/Logiciels/amber11-at1.5/bin/mmpbsa_py_energy for GB
> calculations
> mmpbsa_py_energy found! Using
> /home/joseph/Logiciels/amber11-at1.5/bin/mmpbsa_py_energy for PB
> calculations
> Preparing trajectories for simulation...
> Mutating trajectories...
> Traceback (most recent call last):
> File
> "/home/joseph/Logiciels/amber11-at1.5/AmberTools/src/mmpbsa_py/MMPBSA.py",
> line 938, in <module>
> isinerr = com_muttraj.MutateTraj('_MMPBSA_mutant_complex%s' % trjsuffix)
> File
> "/home/joseph/Logiciels/amber11-at1.5/AmberTools/src/mmpbsa_py/MMPBSA_mods/alamdcrd.py",
> line 276, in MutateTraj
> new_coords = self._mutate(orig_resname, coords_tomutate)
> File
> "/home/joseph/Logiciels/amber11-at1.5/AmberTools/src/mmpbsa_py/MMPBSA_mods/alamdcrd.py",
> line 374, in _mutate
> new_coords.append(coords_received[x+3])
> NameError: global name 'x' is not defined
>
> There seems to be a bug in the python code of alamdcrd.py. After a
> quick look at the code, I suppose that the variable "x" is not correct
> and (looking at the rest of the function) should be "i" instead. I've
> changed the variable name from "x" to "i" and it works.
>
> I guess developers should have a look at it before someone changes the
> python code.
> I hope it will help, MMPBSA is a great tool.
>
> Best regards
>
> --
> Joseph ANDRE
> Ph.D. Student
> SABNP U819 - Groupe de Modélisation Moléculaire
> Université d'Evry
> Rue du Père Jarlan
> 91025 EVRY CEDEX
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
Graduate Student
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Tue Apr 26 2011 - 06:30:03 PDT
