Sean,
You either have a structural clash or your prmtop file mismatch your inpcrd
files. Try to visualize your snapshots in VMD. If you see garbled
structures, you have a mismatch ...
All the best,
Ray
==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo.uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf
Of Sean Zhao
Sent: Thursday, May 07, 2009 6:30 PM
To: amber.ambermd.org
Subject: [AMBER] Problems in the result of MM_PBSA
Hello !
I used Amber 9 to simulate a small molecule bound in a protein. After I have
finished the MM_PBSA, I found the result ( shown below ) was very
unreasonable. For instance, the delta VDW, INT, GAS, PBTOT and GBTOT are all
beyond 10 million. However, no error was reported in the terminal when I was
running the MM_PBSA. How can I fix this issue? Any response will be
appreciated.
Thanks in advance!
Sean
May 8, 2009
# COMPLEX RECEPTOR LIGAND
# ----------------------- -----------------------
-----------------------
# MEAN STD MEAN STD MEAN
STD
# ======================= =======================
=======================
ELE -2582.91 64.34 -3497.80 109.83 203.89
7.71
VDW -550.98 22.86 10037286.88 13997.12 840507.41
1787.90
INT 3434.99 36.17 10647284.69 171501.99 369629.85
66182.10
GAS 301.10 78.00 20681073.77 171650.64 1210341.14
66044.69
PBSUR 75.75 1.36 79.99 1.52 4.16
0.08
PBCAL -1862.76 63.16 -4221.92 465.73 -288.78
10.77
PBSOL -1787.01 62.41 -4141.93 465.72 -284.62
10.71
PBELE -4445.67 19.85 -7719.72 472.86 -84.89
6.53
PBTOT -1485.91 41.18 20676931.84 171666.18 1210056.52
66035.37
GBSUR 76.89 1.68 65.79 1.55 1.86
0.03
GB -1895.65 60.76 -2959.17 82.00 -333.06
10.43
GBSOL -1818.76 59.94 -2893.38 81.36 -331.21
10.43
GBELE -4478.56 16.84 -6456.96 86.75 -129.17
5.51
GBTOT -1517.66 38.80 20678180.40 171636.15 1210009.93
66035.56
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE 711.00 128.38
VDW -10878345.27 14192.28
INT -11013479.55 180264.62
GAS -21891113.81 180114.71
PBSUR -8.40 0.52
PBCAL 2647.94 467.53
PBSOL 2639.54 467.51
PBELE 3358.94 474.91
PBTOT -21888474.27 180141.24
GBSUR 9.25 0.93
GB 1396.58 90.05
GBSOL 1405.82 89.90
GBELE 2107.58 87.06
GBTOT -21889707.99 180104.00
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Received on Wed May 20 2009 - 15:06:40 PDT
