Dear Dr Luo,
Thank you for your helpful comments. VMD visualization of snapshot is "normal", ie no bond/atom break-up. I tried to do what you suggested "use one snapshot to run the job by hand". I took snapshot of complex [A+C] +B, then am attempting to perform production run. But I need to put back water molecules. How to do this ? What do you mean run the job by hand ?
Amor
--- On Fri, 2/7/10, Ray Luo <ray.luo.uci.edu> wrote:
From: Ray Luo <ray.luo.uci.edu>
Subject: Re: [AMBER] mmgbsa tricky output
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Friday, 2 July, 2010, 6:46 AM
There seems to be some inconsistency in your case labeled as "[A+C] +
B". In a single trajectory mmpbsa run, the INT DELTA energy is very
close to zero due to "perfect" cancellation between the internal energy
terms before and after binding. This is the case for case "[A+B] + C",
but not for "[A+C] + B". Another observation is that EEL DELTA should be
mostly canceled out by GB DELTA upon binding. Again, this is the case
for case "[A+B] + C", but not for "[A+C] + B". It might be that your
[A+C] and B trajectories were not generated properly. Visualization in
VMD always helps in this regards. If the trajectories are okay, you
might want to use one snapshot to run the job by hand to find out why ...
Good luck!
Ray
==========================================
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/
==========================================
Amor San Juan wrote:
> 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 Sun Jul 04 2010 - 21:00:03 PDT
