On Fri, Aug 31, 2012 at 9:50 AM, Jan-Philip Gehrcke <jgehrcke.googlemail.com
> wrote:
> On 08/29/2012 04:17 PM, Jason Swails wrote:
> > To be honest, I'm not sure where the error is coming from. Error
> messages
> > in this case seem to be swallowed up (unless they aren't -- are there any
> > errors printed out in the _MMPBSA_complex_pb.mdout.0 file?).
>
> This is the whole content of this mdout file:
>
>
> > Reading parm file (../../complex_unsolvated.prmtop)
> > title:
> >
> > 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 --> 481.891
> > eff.c(2661) eel14 --> 4625.482
>
>
>
> > There were
> > significant changes to PBSA, and my guess is you're hitting a bomb in the
> > code that is forcing a bail-out. Since the PBSA code used by sander and
> > NAB are the same, I would not expect use_sander to fix this.
> >
> > The best bet, IMO, would be to run the energy calc for your complex by
> > hand, and see if MMPBSA.py is inadvertently squashing the error message
> (in
> > which case, this should be fixed). The command for PB should be:
> >
> > mmpbsa_py_energy -O -i _MMPBSA_pb.mdin -p <complex_prmtop> -c
> > _MMPBSA_complex.pdb -y _MMPBSA_complex.mdcrd.0 -o output
> >
> > (mdcrd replaced by nc if you use netcdf intermediates).
> >
> > I'd be interested to see what you learn.
>
>
> You were right about swallowed error messages. We learned something :-).
> See:
>
> > $ mmpbsa_py_energy -i _MMPBSA_pb.mdin -p ../../complex_unsolvated.prmtop
> -c _MMPBSA_complex.pdb -y _MMPBSA_complex.mdcrd.0 -o output
> > PB Bomb in pb_aaradi(): No radius assigned for atom 2021 C1 CG
>
OK. My intent was to capture printed stderr within Python and redirect it
back to the system standard error stream.
I've always liked the idea of sending error messages to stderr, although it
may be helpful to send it to both streams so users know *where* in program
execution the error occurred (although this should be obvious or
unnecessary from the error message itself).
What this error says is that this particular atom, C1 type (CG name, I
think -- you can use "printDetails .2021" in parmed.py to check the full
atomic details of this atom), was not assigned a radius.
What force field are you using? Where might this atom type be coming from?
(e.g., ff99SB, ff99SBildn, ff12SB, ... etc.)
The solution would be to add this atom type explicitly to the PBSA source
code so it assigns the correct radius. The relevant subroutine is
pb_aaradi in $AMBERHOME/AmberTools/src/pbsa/sa_driver.F90.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Aug 31 2012 - 07:30:03 PDT
