[AMBER] mmpbsa.py error

From: George Tzotzos <gtzotzos.me.com>
Date: Mon, 11 May 2015 20:52:04 +0200

Iím 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 11 2015 - 12:00:03 PDT
Custom Search