Dear Amber experts,
I tried running an MMPBSA study on a certain set of topology/trajectory
files. While keeping the input constant, using MMPBSA from AmberTools the analysis works. Using MMPBSA.py from AmberTools 12,
mmpbsa_py_energy crashes with a CalcError:
> Running command:
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp 1err.solvated.prmtop -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y *.mdcrd
> Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /home/taghdir/program/amber12/bin/mmpbsa_py_energy
cpptraj found! Using /home/taghdir/program/amber12/bin/cpptraj
mmpbsa_py_nabnmode found! Using /home/taghdir/program/amber12/bin/mmpbsa_py_nabnmode
Preparing trajectories for simulation...
250 frames were processed by cpptraj for use in calculation.
16 frames were processed by cpptraj for nmode calculations.
Running calculations on normal system...
Beginning PB calculations with /home/taghdir/program/amber12/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning nmode calculations with /home/taghdir/program/amber12/bin/mmpbsa_py_nabnmode
calculating complex contribution...
Line minimizer aborted: step at upper bound 0.00052918458
Line minimizer aborted: step at upper bound 0.042861532
Line minimizer aborted: step at upper bound 0.045932138
Line minimizer aborted: step at upper bound 0.075656689
Line minimizer aborted: step at upper bound 0.0017056896
Line minimizer aborted: step at upper bound 0.0014822023
Line minimizer aborted: step at upper bound 0.0013489239
Line minimizer aborted: step at upper bound 0.0046798647
Line minimizer aborted: step at upper bound 0.032355796
Line minimizer aborted: step at upper bound 0.001812744
Line minimizer aborted: step at upper bound 0.060527145
Line minimizer aborted: step at upper bound 0.071094317
Line minimizer aborted: step at upper bound 0.011856926
Line minimizer aborted: step at upper bound 0.0029842933
Line minimizer aborted: step at upper bound 0.0031832032
Line minimizer aborted: step at upper bound 0.044833858
Line minimizer aborted: step at upper bound 0.0015072489
Line minimizer aborted: step at upper bound 0.008666436
Line minimizer aborted: step at upper bound 0.047428839
Line minimizer aborted: step at upper bound 0.00010246152
Line minimizer aborted: step at upper bound 0.00049122015
Line minimizer aborted: step at upper bound 0.00077474005
Line minimizer aborted: step at upper bound 0.27571959
FETAL:allocationfailed in vector()
> CalcError: /home/taghdir/program/amber/12/bin/mmpbsa_py_energy failed with prmtop complex.prmtop!
I am running this using amber12 and ambertools12
I would be thankful for any sort of help!
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Received on Sat Jun 25 2016 - 23:30:03 PDT
