Hello Amber Users,
i am facing a problem while performing Alanine
scanning mutagenesis.
I am running this command
*$AMBERHOME/bin/MMPBSA.py -O -i alscan.in <
http://alscan.in> -sp
../complex_solvated.prmtop -cp ../complex.prmtop -rp ../pro.prmtop -lp
../lig.prmtop -y ../prod.inpcrd -mc mcom.top -mr mrec.top*
And I am getting some Attribute error as follows:
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using
/apps/gnu/gcc-4.8.5-4/amber/16/amber16/bin/mmpbsa_py_energy
cpptraj found! Using /apps/gnu/gcc-4.8.5-4/amber/16/amber16/bin/cpptraj
Preparing trajectories for simulation...
Mutating trajectories...
File "/apps/gnu/gcc-4.8.5-4/amber/16/amber16//bin/MMPBSA.py", line 99, in
<module>
app.file_setup()
File
"/apps/gnu/gcc-4.8.5-4/amber/amber16/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 169, in file_setup
self.normal_system, self.mutant_system, self.pre)
File
"/apps/gnu/gcc-4.8.5-4/amber/amber16/amber16/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py",
line 324, in make_mutant_trajectories
norm_sys.complex_prmtop, mut_sys.complex_prmtop)
File
"/apps/gnu/gcc-4.8.5-4/amber/amber16/amber16/lib/python2.7/site-packages/MMPBSA_mods/alamdcrd.py",
line 173, in __init__
self.mutres = self.FindMutantResidue()
File
"/apps/gnu/gcc-4.8.5-4/amber/amber16/amber16/lib/python2.7/site-packages/MMPBSA_mods/alamdcrd.py",
line 196, in FindMutantResidue
(self.new_prm.prm_name, self.orig_prm.prm_name))
*AttributeError: 'AmberParm' object has no attribute 'prm_name'*
Exiting. All files have been retained.
Please suggest me the probable reasons.
Thanks..!!
--
*Mitul SrivastavaSenior Research FellowD*rug *D*iscovery *R*esearch *C*enter
(DDRC)
*T*ranslational *H*ealth *S*cience and *T*echnology *I*nstitute (THSTI),
NCR Biotech Science Cluster
3rd Milestone, Faridabad – Gurgaon Expressway
PO box #04, Faridabad – 121001, India
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Received on Thu Jul 05 2018 - 01:00:02 PDT
