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 - 08:58:09 PDT
