geyan
I have faced this problem and it turns out that I did not patch bugfixes properly. Maybe you can try to run the Examples for test.
--- 10年1月21日，周四, geyan <geyan.big.ac.cn> 写道：
发件人: geyan <geyan.big.ac.cn>
主题: [AMBER] need help in MM_PBSA calculation
收件人: "amber" <amber.ambermd.org>
日期: 2010年1月21日,周四,下午5:20
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 - 05:00:03 PST
