Hi,
Can you visualize the trajectory _MMPBSA_complex.(mdcrd/nc) depeding on if
you used the netcdf option and tell me if the same problem occurs. If you
could also look at _MMPBSA_ptraj1.out and see if any errors are in the file.
On Tue, Jul 12, 2011 at 4:19 PM, manikanthan bhavaraju <
manikanthanbhavaraju.gmail.com> wrote:
> The MMPBSA.py script is consistently crashing while analyzing
> _MMPBSA_complex_gb.mdout. The following is written in the .mdout
>
> Reading parm file (com.top)
> title:
>
>
> 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=0.103952
> bad number of bonds to C: 3044 1; using default carbon parameters
> bad number of bonds to C: 3051 1; using default carbon parameters
> bad number of bonds to C: 3055 1; using default carbon parameters
> Processing ASCII trajectory (_MMPBSA_complex.mdcrd)
>
> Processing frame 1
> iter Total bad vdW elect nonpolar genBorn
> frms
> eff.c(3678) enb14 --> 1951.115
> eff.c(3679) eel14 --> 18106.965
> eff.c(3737) enb --> -4318.441
> eff.c(3738) eel --> -35895.304
> eff.c(3739) e_gb --> -4932.438
> eff.c(3740) esurf --> 177.234
> eff.c(3741) evdwnp --> 0.000
> ff: 0 -13689.29 11221.58 -2367.33 -17788.34 177.23 -4932.44
> 1.81e+01
>
> The job got crashed after processing 1st frame.
>
> In VMD I have visualized _MMPBSA_complex.pdb, the atoms 3044, 3051, and
> 3055
> are not bonded to C atom. Why it is showing this error?
>
>
>
> Thanks,
> mani
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--
T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
Graduate Student
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Tue Jul 12 2011 - 14:00:02 PDT
