This almost always means that your trajectory files and your topology files
do not match up. In fact, I've never seen an instance where this is _not_
the case. I suggest you visualize the trajectories that MMPBSA.py
generated with your topology files to see if they look warped or distorted
(I'm guessing they will).
I also suggest that you upgrade to AmberTools 12.0 (you'll need to set the
variable search_path=1 in the &general section to use sander from Amber
11). This version of MMPBSA.py has better topology-file error-checking,
and may provide more information about what is happening. (I don't have
enough information to tell here).
HTH,
Jason
On Sat, Apr 14, 2012 at 7:57 AM, zhangaidi <zhangaidi.mail.kiz.ac.cn> wrote:
>
> Hello,
> Thanks for your response, yes, just like what you say,there are some
> fields
> that are filled with ****s in my _MMPBSA_*.mdout.# files, no matter the
> _MMPBSA_receptor_pb.mdout or _MMPBSA_complex_pb.mdout, some of the detail
> you can see below, Does that matter to parse the output files? . and I
> have
> attached the MMPBSA_*.mdout file
> PRINT DECOMP - TOTAL ENERGIES
>
> resid |internal |vdw |eel |pol |sas
> ============================================================
> TDC 71 ********* 22985.479 -211.087 37.551 0.000
> TDC 83 21939.170 ********* -11.753 -5.234 0.000
> TDC 202 9778.641 22893.201 -3.621 -6.300 0.000
> TDC 204 7199.944 8695.023 -61.212 -5.701 0.000
> TDC 475 55780.250 ********* 14.554 -46.247 0.000
> TDC 476 ********* ********* -163.972 -207.130 0.000
>
> PRINT DECOMP - SIDECHAIN ENERGIES
>
> resid |internal |vdw |eel |pol |sas
> ============================================================
> SDC 71 67852.243 3535.770 -209.468 44.886 0.000
> SDC 83 5819.594 ********* -14.784 -1.252 0.000
> SDC 202 3880.064 10291.709 1.117 0.264 0.000
> SDC 204 2325.367 3319.907 -26.252 4.095 0.000
> SDC 475 55780.250 ********* 14.554 -46.247 0.000
> SDC 476 ********* ********* -163.972 -207.130 0.000
>
> PRINT DECOMP - BACKBONE ENERGIES
>
> resid |internal |vdw |eel |pol |sas
> ============================================================
> BDC 71 32451.845 19449.709 -1.618 -7.335 0.000
> BDC 83 16119.576 ********* 3.031 -3.982 0.000
> BDC 202 5898.577 12601.492 -4.738 -6.564 0.000
> BDC 204 4874.577 5375.116 -34.959 -9.796 0.000
> BDC 475 0.000 0.000 0.000 0.000 0.000
> BDC 476 0.000 0.000 0.000 0.000 0.000
> All comments will be welcome.
> zhang aidi
>
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>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Apr 14 2012 - 09:00:05 PDT
