AMBER Archive (2009)

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

From: Maryam Hamzehee (maryam_h_7860_at_yahoo.com)
Date: Sat Jun 13 2009 - 08:56:16 CDT

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_at_yahoo.com.cn> wrote:

From: 廖青华 <fantastic_0919_at_yahoo.com.cn>
Subject: 回复： [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 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_at_yahoo.com.cn or fantasticqhl_at_yahoo.com

________________________________
发件人： Maryam Hamzehee <maryam_h_7860_at_yahoo.com>
收件人： amber_at_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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