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 pdb file of my complex are the same as the numbers of NTOTAL, LSTART, LSTOP, RSTART and RSTOP. I do not know what is wrong with it.
>
> Thanks
> Maryam
>
>
>
>
> --- On Sat, 6/13/09, 廖青华 <fantastic_0919.yahoo.com.cn> wrote:
>
>
> From: 廖青华 <fantastic_0919.yahoo.com.cn>
> Subject: 回复： 回复： [AMBER] too high in binding energy (MM-PBSA)
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Saturday, June 13, 2009, 7:53 PM
>
>
> Hi, sir,
> Yes, "extract_coords.mmpbsa" file is the same as "mm_pbsa.in" file , both are the input files of the mm_pbsa calculation, with different file names. 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 the numbers in the pdb file of your complex is the same as the numbers of NTOTAL, LSTART, LSTOP, RSTART and RSTOP.
>
> Good luck!
>
> Qinghua Liao
>
> fantastic_0919.yahoo.com.cn or fantasticqhl.yahoo.com
>
>
>
>
> ________________________________
> 发件人： Maryam Hamzehee <maryam_h_7860.yahoo.com>
> 收件人： AMBER Mailing List <amber.ambermd.org>
> 已发送： 2009/6/13(周六), 下午9:56:16
> 主题： Re: 回复： [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 file, do you mean "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.
>
> All the best,
> Maryam
>
> --- On Sat, 6/13/09, 廖青华 <fantastic_0919.yahoo.com.cn> wrote:
>
>
> From: 廖青华 <fantastic_0919.yahoo.com.cn>
> Subject: 回复： [AMBER] too high in binding energy (MM-PBSA)
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Saturday, June 13, 2009, 5:14 PM
>
>
> Hi Maryam Hamzehee,
> I also encountered the same problem 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. You should check it by regenerating the pdb file from your *.prmtop and *.inpcrd files of complex using command ambpdb.
>
> Good luck!
>
> Qinghua Liao
>
> fantastic_0919.yahoo.com.cn or fantasticqhl.yahoo.com
>
>
>
>
> ________________________________
> 发件人： Maryam Hamzehee <maryam_h_7860.yahoo.com>
> 收件人： amber.ambermd.org
> 已发送： 2009/6/13(周六), 下午5:53:43
> 主题： [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 “Tutorial A3: MM-PBSA”. I have performed the MD for the ligand-protein complex up to 4ns, the results are shown below:
>
> # COMPLEX RECEPTOR LIGAND
> # ----------------------- ----------------------- ---------------------
> --
> # MEAN STD MEAN STD MEAN S
> TD
> # ======================= ======================= =====================
> ==
> ELE -17522.63 140.50 -15680.04 175.32 -1464.72 72.88
> VDW -2184.97 35.92 16218.97 94.50 1019955.82 28749.20
> INT 11460.75 67.35 10503.06 63.03 3397603.93 535323.59
> GAS -8246.85 147.21 11041.99 212.12 4416095.03 537408.13
> PBSUR 211.35 1.93 203.32 1.85 33.58 0.64
> PBCAL -6424.57 128.02 -6187.77 156.53 -2137.68 213.57
> PBSOL -6213.22 127.07 -5984.45 155.42 -2104.10 213.53
> PBELE -23947.20 46.55 -21867.81 47.02 -3602.40 205.89
> PBTOT -14460.07 68.33 5057.54 112.99 4413990.93 537351.27
> GBSUR 211.35 1.93 203.32 1.85 33.58 0.64
> GB -6537.48 130.17 -6309.73 157.62 -1630.23 44.54
> GBSOL -6326.13 129.22 -6106.41 156.51 -1596.65 44.33
> GBELE -24060.11 39.42 -21989.77 40.38 -3094.95 62.88
> GBTOT -14572.98 67.59 4935.58 113.98 4414498.38 537397.88
> # DELTA
> # -----------------------
> # MEAN STD
> # =======================
> ELE -377.88 122.64
> VDW -1038359.76 28742.84
> INT -3396646.24 535320.32
> GAS -4435383.87 537455.24
> PBSUR -25.56 1.02
> PBCAL 1900.89 247.22
> PBSOL 1875.33 246.84
> PBELE 1523.01 204.69
> PBTOT -4433508.54 537355.75
> GBSUR -25.56 1.02
> GB 1402.49 122.13
> GBSOL 1376.93 121.44
> GBELE 1024.61 62.02
> GBTOT -4434006.94 537403.59
>
> 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.
>
> Any help in this regard would be highly appreciated,
>
> Cheers,
> Maryam
>
>
>
>
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Received on Mon Jul 06 2009 - 08:59:37 PDT
