I’m trying to find deltaG of a homodimer.
The dimer contains chains A (res 1-125) and B (res 127-151), two conserved water molecules (res 153,154) and two ligands (res 126, res 152).
I used ante-mmpbsa.py to generate new topologies:
ante-mmpbsa.py -p complex_solv.prmtop -s :126,252-254,WAT,Na+ -c subA-subB.prmtop -m :1-125 -r subA.prmtop -l subB.prmtop --radii=mbondi2
I tried to run mmpbsa.py (serial) for a short 10 frame trajectory as test.
MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp complex_solv.prmtop -cp subA-subB.prmtop -rp subA.prmtop -lp subB.prmtop -y 10frame.nc
mmpbsa.py aborts on reading the receptor.prmtop
CalcError: /Users/gtzotzos/Programs/MD/amber12/bin/cpptraj failed with prmtop subA.prmtop!
Reading the cpptraj parminfo output, the topologies appear to be correct:
Topology complex_solv.prmtop contains 42239 atoms.
12995 residues.
42283 bonds.
12747 molecules.
Box: Trunc. Oct.
12725 solvent molecules.
Final solute residue is 270
> parm subA-subB.prmtop
AmberParm Title: [default_name]
Radius Set: H(N)-modified Bondi radii (mbondi2)
> parminfo
Topology subA-subB.prmtop contains 3984 atoms.
250 residues.
4046 bonds.
2 molecules.
Box: None
> parm subA.prmtop
AmberParm Title: [default_name]
Radius Set: H(N)-modified Bondi radii (mbondi2)
> parminfo
Topology subA.prmtop contains 1992 atoms.
125 residues.
2023 bonds.
1 molecules.
Box: None
parm subB.prmtop
AmberParm Title: [default_name]
Radius Set: H(N)-modified Bondi radii (mbondi2)
> parminfo
Topology subB.prmtop contains 1992 atoms.
125 residues.
2023 bonds.
1 molecules.
Box: None
> parm complex_solv.prmtop
AmberParm Title: [default_name]
Radius Set: H(N)-modified Bondi radii (mbondi2)
> parminfo
Topology complex_solv.prmtop contains 42239 atoms.
12995 residues.
42283 bonds.
12747 molecules.
Box: Trunc. Oct.
12725 solvent molecules.
Final solute residue is 270
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Received on Mon May 11 2015 - 12:00:03 PDT
