Jonathan,
Set inp=1 and radiopt=0 in your input file should get it over ...
Ray
On Mon, Dec 3, 2012 at 3:13 PM, Jonathan Gough
<jonathan.d.gough.gmail.com> wrote:
> 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
