Dear Amber users
I am facing a problem using MMPBSA.py while calculating GBSA
MMPBSA.py -O -i mmpbsa_e.in -o result_e.dat -sp topol_wild_nowat.prmtop
-cp com.prmtop -rp rec.prmtop -lp ligand.prmtop -y wild_fixedcorrupted.nc
Loading and checking parameter files for compatibility...
cpptraj found! Using /opt/amber18/bin/cpptraj
mmpbsa_py_energy found! Using /opt/amber18/bin/mmpbsa_py_energy
Preparing trajectories for simulation...
File "/opt/amber18/bin/MMPBSA.py", line 99, in <module>
app.file_setup()
File "/opt/anaconda/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 169, in file_setup
self.normal_system, self.mutant_system, self.pre)
File
"/opt/anaconda/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py", line
298, in make_mutant_trajectories
from alamdcrd import MutantMdcrd, GlyMutantMdcrd
ModuleNotFoundError: No module named 'alamdcrd'
Exiting. All files have been retained.
The input file I used is as follows:-
&general
startframe=1, endframe=8060, interval=100
strip_mask= :WAT,Na+,
/
&gb
igb=5, saltcon=0.150
/
I am not getting why this error is arising and how can I fix it. Could you
please give me any suggestions to fix this error?
Thanks in advance.
Sadaf
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Received on Thu Sep 09 2021 - 07:30:02 PDT
