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
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Received on Tue Apr 26 2011 - 03:00:05 PDT
