AMBER Archive (2009)

Subject: Re: 回复： 回复： [AMBER] too high in binding energy (MM-PBSA)

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Sat Jun 13 2009 - 13:19:09 CDT

Maryam,

I assume that you created the coordinate files before calculating the
binding free energy. In the tutorial, first you extract the coordinate
files, and then you use those files for the binding free energy
calculation. Can you check out one of the snapshot of the
ligand, receptor, and complex? If the prmtop files are correct, the
structures should resemble the ligand, receptor, and complex,
respectively.

   Ilyas Yildirim, Ph.D.
   ---------------------------------------------------------------
   = Hutchison Hall B#10 - Department of Chemistry =
   = - University of Rochester =
   = 585-275-6766 (office) - =
   = http://www.pas.rochester.edu/~yildirim/ =
   ---------------------------------------------------------------

On Sat, 13 Jun 2009, Maryam Hamzehee wrote:

> Hi Qinghua
> I rechecked those numbers mentioned in previous emails, numbers in the聽pdb file of my complex聽are the same as the numbers of NTOTAL, LSTART, LSTOP, RSTART and RSTOP. I do not know what is wrong with it.
> 聽
> Thanks
> Maryam
> 聽
>
>
>
> --- On Sat, 6/13/09, 寤栭潚鍗 <fantastic_0919_at_yahoo.com.cn> wrote:
>
>
> From: 寤栭潚鍗 <fantastic_0919_at_yahoo.com.cn>
> Subject: 鍥炲锛 鍥炲锛 [AMBER] too high in binding energy (MM-PBSA)
> To: "AMBER Mailing List" <amber_at_ambermd.org>
> Date: Saturday, June 13, 2009, 7:53 PM
>
>
> Hi, sir,
> Yes, "extract_coords.mmpbsa" file聽is the same as "mm_pbsa.in" file聽, both are the input files of the mm_pbsa calculation, with different file names.聽I thought that it was not problems of your files, but problems of NTOTAL, LSTART, LSTOP, RSTART and RSTOP. You can re-check it with the vim tool in linux to see whether聽the numbers in the聽聽pdb file of your complex is the same as the numbers of NTOTAL, LSTART, LSTOP, RSTART and RSTOP.
>
> Good luck!
>
> Qinghua Liao
>
> fantastic_0919_at_yahoo.com.cn or fantasticqhl_at_yahoo.com
>
>
>
>
> ________________________________
> 鍙戜欢浜猴細 Maryam Hamzehee <maryam_h_7860_at_yahoo.com>
> 鏀朵欢浜猴細 AMBER Mailing List <amber_at_ambermd.org>
> 宸插彂閫侊細 2009/6/13(鍛ㄥ叚), 涓嬪崍9:56:16
> 涓婚锛 Re: 鍥炲锛 [AMBER] too high in binding energy (MM-PBSA)
>
> Dear Qinghua
> Many thanks for your email, you have suggested that there is a problem with "mm_pbsa.in" file but I do not have such聽file, do聽you mean 聽"extract_coords.mmpbsa" file (according to the tutorial TUTORIAL A3: MM-PBSA). I checked this file and I realized that the number of receptor and ligand and number of atoms (i.e. NTOTAL, LSTART, LSTOP, RSTART and RSTOP and etc) were O.K. Subsequently, I converted the *.prmtop and *.inpcrd to *.pdb file; I visualized them but there are not any problem with those files. Also, I converted *.mdcrd to *.binpos and I visualized trajectory file with VMD; Similarly, there is not any wrong with it.
> 聽
> All the best,
> Maryam
>
> --- On Sat, 6/13/09, 寤栭潚鍗 <fantastic_0919_at_yahoo.com.cn> wrote:
>
>
> From: 寤栭潚鍗 <fantastic_0919_at_yahoo.com.cn>
> Subject: 鍥炲锛 [AMBER] too high in binding energy (MM-PBSA)
> To: "AMBER Mailing List" <amber_at_ambermd.org>
> Date: Saturday, June 13, 2009, 5:14 PM
>
>
> Hi Maryam Hamzehee,
> I also encountered the same problem聽you put forward in the last mail. The problem is mainly because something wrong with your input file, mm_pbsa.in.
> You have filled the wrong number of the receptor and ligand, I think.聽You should check it by regenerating the pdb file from your *.prmtop and *.inpcrd files of complex聽using command ambpdb.
> 聽
> Good luck!
> 聽
> Qinghua Liao
>
> 聽fantastic_0919_at_yahoo.com.cn or fantasticqhl_at_yahoo.com
>
>
>
>
> ________________________________
> 鍙戜欢浜猴細 Maryam Hamzehee <maryam_h_7860_at_yahoo.com>
> 鏀朵欢浜猴細 amber_at_ambermd.org
> 宸插彂閫侊細 2009/6/13(鍛ㄥ叚), 涓嬪崍5:53:43
> 涓婚锛 [AMBER] too high in binding energy (MM-PBSA)
>
> Dear All
> I am doing a simulation to calculate binding energy for a complex almost in a similar way to that mentioned for 鈥淭utorial A3: MM-PBSA鈥. 聽I have performed the MD for the ligand-protein complex up to 4ns, the results are shown below:
> 聽
> #聽聽聽聽聽聽聽聽聽聽聽聽聽聽聽聽聽 COMPLEX聽聽聽聽聽聽聽聽聽聽聽聽聽聽聽 RECEPTOR聽聽聽聽聽聽聽聽聽聽聽聽聽聽聽聽聽 LIGAND
> #聽聽聽聽聽聽聽聽聽 ----------------------- ----------------------- ---------------------
> --
> #聽聽聽聽聽聽聽聽聽聽聽聽聽聽聽聽聽 MEAN聽聽聽聽聽聽聽 STD聽聽聽聽聽聽聽聽 MEAN聽聽聽聽聽聽聽 STD聽聽聽聽聽聽聽聽 MEAN聽聽聽聽聽聽聽 S
> TD
> #聽聽聽聽聽聽聽聽聽 ======================= ======================= =====================
> ==
> ELE聽聽聽聽聽聽聽聽聽聽 -17522.63聽聽聽聽 140.50聽聽聽 -15680.04聽聽聽聽 175.32聽聽聽聽 -1464.72聽聽聽聽聽 72.88
> VDW聽聽聽聽聽聽聽聽聽聽聽 -2184.97聽聽聽聽聽 35.92聽聽聽聽 16218.97聽聽聽聽聽 94.50聽聽 1019955.82聽聽 28749.20
> INT聽聽聽聽聽聽聽聽聽聽聽 11460.75聽聽聽聽聽 67.35聽聽聽聽 10503.06聽聽聽聽聽 63.03聽聽 3397603.93聽 535323.59
> GAS聽聽聽聽聽聽聽聽聽聽聽 -8246.85聽聽聽聽 147.21聽聽聽聽 11041.99聽聽聽聽 212.12聽聽 4416095.03聽 537408.13
> PBSUR聽聽聽聽聽聽聽聽聽聽聽 211.35聽聽聽聽聽聽 1.93聽聽聽聽聽聽 203.32聽聽聽聽聽聽 1.85聽聽聽聽聽聽聽 33.58聽聽聽聽聽聽 0.64
> PBCAL聽聽聽聽聽聽聽聽聽 -6424.57聽聽聽聽 128.02聽聽聽聽 -6187.77聽聽聽聽 156.53聽聽聽聽 -2137.68聽聽聽聽 213.57
> PBSOL聽聽聽聽聽聽聽聽聽 -6213.22聽聽聽聽 127.07聽聽聽聽 -5984.45聽聽聽聽 155.42聽聽聽聽 -2104.10聽聽聽聽 213.53
> PBELE聽聽聽聽聽聽聽聽 -23947.20聽聽聽聽聽 46.55聽聽聽 -21867.81聽聽聽聽聽 47.02聽聽聽聽 -3602.40聽聽聽聽 205.89
> PBTOT聽聽聽聽聽聽聽聽 -14460.07聽聽聽聽聽 68.33聽聽聽聽聽 5057.54聽聽聽聽 112.99聽聽 4413990.93聽 537351.27
> GBSUR聽聽聽聽聽聽聽聽聽聽聽 211.35聽聽聽聽聽聽 1.93聽聽聽聽聽聽 203.32聽聽聽聽聽聽 1.85聽聽聽聽聽聽聽 33.58聽聽聽聽聽聽 0.64
> GB聽聽聽聽聽聽聽聽聽聽聽聽 -6537.48聽聽聽聽 130.17聽聽聽聽 -6309.73聽聽聽聽 157.62聽聽聽聽 -1630.23聽聽聽聽聽 44.54
> GBSOL聽聽聽聽聽聽聽聽聽 -6326.13聽聽聽聽 129.22聽聽聽聽 -6106.41聽聽聽聽 156.51聽聽聽聽 -1596.65聽聽聽聽聽 44.33
> GBELE聽聽聽聽聽聽聽聽 -24060.11聽聽聽聽聽 39.42聽聽聽 -21989.77聽聽聽聽聽 40.38聽聽聽聽 -3094.95聽聽聽聽聽 62.88
> GBTOT聽聽聽聽聽聽聽聽 -14572.98聽聽聽聽聽 67.59聽聽聽聽聽 4935.58聽聽聽聽 113.98聽聽 4414498.38聽 537397.88
> #聽聽聽聽聽聽聽聽聽聽聽聽聽聽聽聽聽聽聽 DELTA
> #聽聽聽聽聽聽聽聽聽 -----------------------
> #聽聽聽聽聽聽聽聽聽聽聽聽聽聽聽聽聽 MEAN聽聽聽聽聽聽聽 STD
> #聽聽聽聽聽聽聽聽聽 =======================
> ELE聽聽聽聽聽聽聽聽聽聽聽聽 -377.88聽聽聽聽 122.64
> VDW聽聽聽聽聽聽聽聽 -1038359.76聽聽 28742.84
> INT聽聽聽聽聽聽聽聽 -3396646.24聽 535320.32
> GAS聽聽聽聽聽聽聽聽 -4435383.87聽 537455.24
> PBSUR聽聽聽聽聽聽聽聽聽聽聽 -25.56聽聽聽聽聽聽 1.02
> PBCAL聽聽聽聽聽聽聽聽聽聽 1900.89聽聽聽聽 247.22
> PBSOL聽聽聽聽聽聽聽聽聽聽 1875.33聽聽聽聽 246.84
> PBELE聽聽聽聽聽聽聽聽聽聽 1523.01聽聽聽聽 204.69
> PBTOT聽聽聽聽聽聽 -4433508.54聽 537355.75
> GBSUR聽聽聽聽聽聽聽聽聽聽聽 -25.56聽聽聽聽聽聽 1.02
> GB聽聽聽聽聽聽聽聽聽聽聽聽聽 1402.49聽聽聽聽 122.13
> GBSOL聽聽聽聽聽聽聽聽聽聽 1376.93聽聽聽聽 121.44
> GBELE聽聽聽聽聽聽聽聽聽聽 1024.61聽聽聽聽聽 62.02
> GBTOT聽聽聽聽聽聽 -4434006.94聽 537403.59
> 聽
> As far as I concerned the PBTOT shows the total binding free energy, in our calculation PBTOT is -4433508.54. It is highly negative. I think the large amount of this figure is related to ligand, what is wrong with my simulation.
> 聽
> Any help in this regard would be highly appreciated,
> 聽
> Cheers,
> Maryam
> 聽
>
>
>
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