Can anybody take time to read my post and give any suggestion. Thanks a lot.
--- On Wed, 30/6/10, Amor San Juan <amorsanjuan.yahoo.com> wrote:
From: Amor San Juan <amorsanjuan.yahoo.com>
Subject: [AMBER] mmgbsa tricky output
To: amber.ambermd.org
Date: Wednesday, 30 June, 2010, 5:19 PM
I have protein (A), short peptide (B) and m7GTP (C). I calculated delta-H (enthalpy) using mmgbsa for different systems with results as follows:
1.) A + B = -63.98
2.) A + C = -49.34
3.)[A+B] + C = -48.72
Here is the tricky result when I tried calculating for [A+C] + B using the trajectory from (3) above, I got a value of -1686.27. Detailed values shown below:
[A+B] + C
COMPLEX RECEPTOR LIGAND
[A+B]+C A+B C
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= ======================= =======================
ELE -7290.68 83.95 -6127.91 78.19 -175.61 11.69
VDW -924.90 22.27 -890.49 21.70 -2.34 1.67
INT 4373.96 42.79 4256.68 42.01 117.68 7.44
GAS -3841.62 89.97 -2761.72 85.19 -60.27 12.38
GBSUR 79.51 0.95 80.67 0.94 4.87 0.09
GB -2967.91 71.26 -3318.90 69.23 -625.94 10.99
GBSOL -2888.40 70.96 -3238.24 68.99 -621.07 10.93
GBELE -10258.59 27.43 -9446.81 24.94 -801.55 5.06
GBTOT -6730.02 46.04 -5999.96 44.23 -681.34 5.38
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -987.16 61.60
VDW -32.07 4.79
INT -0.40 0.10
GAS -1019.63 60.60
GBSUR -6.03 0.19
GB 976.94 53.05
GBSOL 970.91 53.03
GBELE -10.23 12.67
GBTOT -48.72 11.11
[A+C]+B
# COMPLEX RECEPTOR LIGAND
[A+C]+B A+C B
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= ======================= =======================
ELE -7290.68 83.95 -5113.57 83.14 -247.41 15.01
VDW -924.90 22.27 -845.52 21.31 -14.26 4.50
INT 4373.96 42.79 4051.41 41.25 255.06 10.75
GAS -3841.62 89.97 -1907.69 89.32 -6.61 17.85
GBSUR 79.51 0.95 76.39 0.89 12.87 0.25
GB -2967.91 71.26 -2705.33 73.00 -513.38 14.14
GBSOL -2888.40 70.96 -2628.94 72.69 -500.52 14.03
GBELE -10258.59 27.43 -7818.91 23.53 -760.79 4.10
GBTOT -6730.02 46.04 -4536.63 42.73 -507.12 10.47
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -1929.70 30.46
VDW -65.12 4.04
INT 67.50 5.02
GAS -1927.33 31.26
GBSUR -9.75 0.33
GB 250.81 26.66
GBSOL 241.06 26.55
GBELE -1678.89 9.39
GBTOT -1686.27 10.80
Problem: As shown in red font, these are the values which is questionable or unrealistic.
My interpretation: ELE value is high which was not offset by small value of GB. Also, INT value is not close to zero (single trajectory calculation). Note that structures of generated coordinates were all looking alright once checked/viewed in vmd.
Attempt to find "right' solution: Implemented igb=5 in mmgbsa, in contrast to igb=2 as used above. Would it make sense ? Try and see ... so below is the result:
[A+C]+B (using igb=5)
# COMPLEX RECEPTOR LIGAND
[A+C]+B A+C B
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= ======================= =======================
ELE -7290.68 83.95 -5113.57 83.14 -247.41 15.01
VDW -924.90 22.27 -845.52 21.31 -14.26 4.50
INT 4373.96 42.79 4051.41 41.25 255.06 10.75
GAS -3841.62 89.97 -1907.69 89.32 -6.61 17.85
GBSUR 79.51 0.95 76.39 0.89 12.87 0.25
GB -1308.03 93.37 -1378.72 85.51 -421.59 13.52
GBSOL -1228.52 93.02 -1302.33 85.18 -408.73 13.41
GBELE -8598.71 72.13 -6492.30 61.17 -669.00 6.02
GBTOT -5070.14 80.22 -3210.02 70.34 -415.33 11.10
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -1929.70 30.46
VDW -65.12 4.04
INT 67.50 5.02
GAS -1927.33 31.26
GBSUR -9.75 0.33
GB 492.29 33.91
GBSOL 482.54 33.82
GBELE -1437.41 23.66
GBTOT -1444.78 24.18
Alright, so as shown in blue font are values that changed upon using igb=5. So, the values isnt still "right".
I would greatly appreciate fresh ideas on how to find a "right" value for [A+C] +B system.
Thank you for all your time.
-amore-
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Received on Thu Jul 01 2010 - 01:00:03 PDT
