one way of analyzing is that
convert them into pdb using "ambpdb"
for all your ABCs in complex as well as separately, by doing that you will come to know whether the scripts ok or properly referred to?
you have to convert individual crds (what ever you are refering for mmgbsa calc) into pdbs
Mannan
--- On Mon, 5/7/10, Amor San Juan <amorsanjuan.yahoo.com> wrote:
From: Amor San Juan <amorsanjuan.yahoo.com>
Subject: Re: [AMBER] mmgbsa tricky output
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Monday, 5 July, 2010, 11:52 AM
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
# ----------------------- ----------------------- -----------------------
# 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
# ----------------------- ----------------------- -----------------------
# 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 the values which is
questionable or unrealistic are ELE, INT, GB, GBELE and GBSOL.
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
# ----------------------- ----------------------- -----------------------
# 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 shownGB, GBSOL, GBELE, GBTOT 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 Wed Jul 07 2010 - 20:30:03 PDT
