AMBER Archive (2009)

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

From: 廖青华 (fantastic_0919_at_yahoo.com.cn)
Date: Sat Jun 13 2009 - 10:23:38 CDT

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_at_yahoo.com.cn or fantasticqhl_at_yahoo.com

________________________________
发件人： Maryam Hamzehee <maryam_h_7860_at_yahoo.com>
收件人： AMBER Mailing List <amber_at_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_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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