HI All.
This error was reported before, but I could not find the solution.
http://archive.ambermd.org/201206/0597.html
the MMPBSA script gets through the GB calculation but crashes out durring
the PB portion.
here is what comes out of the command line:
jonathans-Mac-Pro:prod jonathan$ MMPBSA.py -O -i mmpbsa.in -o
FINAL_RESULTS_MMPBSA.dat -sp eq9-tip3.prmtop -cp equil9.prmtop -rp
3L1Ge9.prmtop -lp peptidee9.prmtop -y prod1.mdcrd
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /Volumes/jonathan/amber12/bin/mmpbsa_py_energy
cpptraj found! Using /Volumes/jonathan/amber12/bin/cpptraj
Preparing trajectories for simulation...
500 frames were processed by cpptraj for use in calculation.
Beginning GB calculations with
/Volumes/jonathan/amber12/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with
/Volumes/jonathan/amber12/bin/mmpbsa_py_energy
calculating complex contribution...
CalcError: /Volumes/jonathan/amber12/bin/mmpbsa_py_energy failed with
prmtop equil9.prmtop!
Exiting. All files have been retained.
inside of _MMPBSA_complex_pb.mdout.0
there is -
Reading parm file (equil9.prmtop)
title:
default_name
mm_options: e_debug=3
mm_options: ipb=2
mm_options: inp=2
mm_options: epsin=1.000000
mm_options: epsout=80.000000
mm_options: smoothopt=1
mm_options: istrng=0.000000
mm_options: radiopt=1
mm_options: dprob=1.400000
mm_options: iprob=2.000000
mm_options: npbopt=0
mm_options: solvopt=1
mm_options: accept=0.001000
mm_options: maxitn=1000
mm_options: fillratio=4.000000
mm_options: space=0.500000
mm_options: nfocus=2
mm_options: fscale=8
mm_options: bcopt=5
mm_options: eneopt=2
mm_options: cutnb=0.000000
mm_options: sprob=0.557000
mm_options: cavity_surften=0.037800
mm_options: cavity_offset=-0.569200
Processing ASCII trajectory (_MMPBSA_complex.mdcrd.0)
Processing frame 1
iter Total bad vdW elect nonpolar EPB
frms
eff.c(2660) enb14 --> 374.278
eff.c(2661) eel14 --> 3426.607
and nothing else. - no errors.
in the similar gb file _MMPBSA_complex_gb.mdout.0
There is:
Reading parm file (equil9.prmtop)
title:
default_name
mm_options: e_debug=2
mm_options: gb=2
mm_options: rgbmax=25.000000
mm_options: gbsa=1
mm_options: surften=0.007200
mm_options: cut=999.000000
mm_options: epsext=78.300000
mm_options: kappa=0.000000
Using carbon SA parms for atom type 2C
Using carbon SA parms for atom type 2C
Using carbon SA parms for atom type 2C
Using carbon SA parms for atom type 3C
Using carbon SA parms for atom type 2C
Using carbon SA parms for atom type 2C
...
Processing ASCII trajectory (_MMPBSA_complex.mdcrd.0)
Processing frame 1
iter Total bad vdW elect nonpolar genBorn
frms
eff.c(2660) enb14 --> 374.278
eff.c(2661) eel14 --> 3426.607
eff.c(2719) enb --> -750.150
eff.c(2720) eel --> -7338.325
eff.c(2721) e_gb --> -1622.060
eff.c(2722) esurf --> 44.491
eff.c(2723) evdwnp --> 0.000
ff: 0 -2800.72 3064.43 -375.87 -3911.72 44.49 -1622.06
1.78e+01
BOND = 326.4088 ANGLE = 946.2504 DIHED =
1791.7755
VDWAALS = -750.1502 EEL = -7338.3248 EGB =
-1622.0603
1-4 VDW = 374.2781 1-4 EEL = 3426.6074 RESTRAINT =
0.0000
ESURF = 44.4909
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Received on Mon Dec 03 2012 - 15:30:04 PST
