Most likely you haven't patched the latest Amber10 bugfixes ... please
make sure you can pass all test cases within $AMBERHOME/src/mmpbsa.
==========================================
Ray Luo, Ph.D.
Associate Professor in Computational
Biochemistry and Molecular Biophysics
Dept of Molecular Biology and Biochemistry
Dept of Biomedical Engineering
University of California, Irvine, CA 92697-3900
Email: rluo.uci.edu Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/rayl/
==========================================
geyan wrote:
> Dear Amber_users,
> I have met a problem in performing the MM_PBSA analysis. Following the MM_PBSA section of Amber tutorial,I can't accomplish the bind_energy calulation
> with the error says,"No data for 0+0 PB ELRAELE 0". Besides,the output file also gives the error message like,"
> WARNING: Missing PBNONPOL for PB in 160 -> Taken from 159
> WARNING: Missing ELRAELE for PB in 160 -> Taken from 159
> WARNING: Missing EPB for PB in 160 -> Taken from 159"
> I searched this problem in Google,finding the solution by changing index 0 of ELRAELE, EPB, PBNONPOL in mm_pbsa_statistics.pm to 0 and
> "Use the snapshot_statistics dot in as the input file, assign an output file
> and if you have the snapshots of com, rec and lig from three different
> trajectories, set calc_delta = 2. If you had extracted the snapshots from
> the same trajectory, set calc_delta = 1. For both cases, you can set
> calc_decomp to 0. " this paragraph is what I directly copy from the internet.
> Truely,it does work in some degree. But after comparing with the exact result download from the tutorial,my result have a clear mistake,that is the item PBSUR and GBSUR is zero in every respect as follows,and other figures is slightly different with the standed result.
> So,just changing the above parameters is not sufficient to solve the problem,can anybody help me? I am very eager to receive your replies.
> Thank you very much!
> GeYan
> # COMPLEX RECEPTOR LIGAND
> # ----------------------- ----------------------- -----------------------
> # MEAN STD MEAN STD MEAN STD
> # ======================= ======================= =======================
> ELE -8656.78 70.18 -5602.09 63.10 -2102.25 52.57
> VDW -984.99 24.34 -661.18 20.33 -256.02 12.93
> INT 5085.33 50.22 3449.57 38.65 1635.76 29.42
> GAS -4556.44 75.96 -2813.70 65.21 -722.52 53.50
> PBSUR 0.00 0.00 0.00 0.00 0.00 0.00
> PBCAL -3244.39 59.67 -2516.48 50.04 -1672.39 47.87
> PBSOL -3244.39 59.67 -2516.48 50.04 -1672.39 47.87
> PBELE -11901.17 33.10 -8118.58 28.08 -3774.64 16.64
> PBTOT -7800.82 48.10 -5330.18 36.70 -2394.91 26.71
> GBSUR 0.00 0.00 0.00 0.00 0.00 0.00
> GB -3250.03 59.24 -2540.49 50.86 -1672.13 48.22
> GBSOL -3250.03 59.24 -2540.49 50.86 -1672.13 48.22
> GBELE -11906.80 27.15 -8142.59 23.52 -3774.38 13.43
> GBTOT -7806.46 47.32 -5354.19 35.95 -2394.64 27.08
> # DELTA
> # -----------------------
> # MEAN STD
> # =======================
> ELE -952.43 44.10
> VDW -67.79 5.18
> INT -0.00 0.00
> GAS -1020.22 44.58
> PBSUR 0.00 0.00
> PBCAL 944.49 43.14
> PBSOL 944.49 43.14
> PBELE -7.95 9.81
> PBTOT -75.73 8.32
> GBSUR 0.00 0.00
> GB 962.59 41.40
> GBSOL 962.59 41.40
> GBELE 10.16 7.77
> GBTOT -57.63 6.52
>
>
>
> 2010-01-21
>
>
>
> geyan
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 21 2010 - 11:00:02 PST
