Hi,
It is not clear as to what is exactly happening and I don't see a
problem with your input as well. The delta INT value you have computed is
equal to 7.73 and it should be 0 or close to it if you are using a *single
trajectory* approach. Make sure that you have properly prepared the topology
files for the complex, ligand, and receptor. My last suggestion is to check
that you have correctly numbered the atoms corresponding to the ligand and
receptor which are used to make the snapshots.
On Sat, Nov 13, 2010 at 10:59 PM, xuemeiwang1103 <xuemeiwang1103.163.com>wrote:
> Dear All :
> I'm sorry for sending this mail again, I still can't solve this
> problem by now, hope someone kind enough to give me some advices. After run
> a short time simulation, I got the value of the binding energy. But it
> seems wrong, the PBTOT is positive.This indicates that my system is not
> stable.The structure is good by using VMD. My input file is below.I am
> confused about this, Could someone tell me how to solve this problem?
> BTW,there is a metal ion near the ligand,the distance is about 5A. I
> used the bonded model and resp charge to simulate the meatal ion. when I
> prapared the initial prmtop fiel for the MMPBSA, I treat the protein and the
> metal ion as the receptor and I still use the bonded model+resp charge
> (eg,the charge of the metal ion is not integral ,it is 0.6e....). I don't
> know if is this caused the strange value.Could someone help me?Thank you
> very much!
> my input file:
> PREFIX snapshot
> PATH ../snap/
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> COMPT ./111.prmtop
> RECPT ./222.prmtop
> LIGPT ./333.prmtop
> GC 0
> AS 0
> DC 0
> MM 1
> GB 1
> PB 1
> MS 1
> NM 0
> .PB
> PROC 2
> REFE 0
> INDI 1.0
> EXDI 80.0
> PRBRAD 1.4
> ISTRNG 0.0
> RADIOPT 0
> NPOPT 1
> CAVITY_SURFTEN 0.0072
> CAVITY_OFFSET 0.00
> SURFTEN 0.0072
> SURFOFF 0.00
> .MM
> DIELC 1.0
> .GB
> IGB 2
> GBSA 1
> SALTCON 0.00
> EXTDIEL 80.0
> INTDIEL 1.0
> SURFTEN 0.0072
> SURFOFF 0.00
> .MS
> PROBE 0.0
> .PROGRAMS
>
> My ouput file:
> # COMPLEX RECEPTOR
> LIGAND
> # ----------------------- -----------------------
> -----------------------
> # MEAN STD MEAN STD MEAN
> STD
> # ======================= =======================
> =======================
> ELE -14104.08 118.29 -14214.13 117.48 6.36
> 4.11
> VDW -2952.56 34.85 -2902.22 34.50 6.00
> 2.05
> INT 12956.05 80.78 12881.95 80.06 66.38
> 5.11
> GAS -4100.59 126.66 -4234.41 125.40 78.74
> 7.00
> PBSUR 174.96 2.55 176.25 2.47 5.11
> 0.05
> PBCAL -6431.77 111.16 -6315.64 109.09 -74.51
> 3.51
> PBSOL -6256.81 109.58 -6139.40 107.60 -69.40
> 3.52
> PBELE -20535.85 48.06 -20529.78 47.63 -68.15
> 1.00
> PBTOT -10357.40 84.52 -10373.81 83.73 9.34
> 5.07
> GBSUR 174.96 2.55 176.25 2.47 5.11
> 0.05
> GB -6603.77 108.13 -6473.90 106.79 -76.45
> 3.77
> GBSOL -6428.81 106.76 -6297.65 105.47 -71.34
> 3.78
> GBELE -20707.85 37.14 -20688.04 37.02 -70.09
> 0.84
> GBTOT -10529.40 77.15 -10532.06 76.75 7.40
> 5.10
> # DELTA
> # -----------------------
> # MEAN STD
> # =======================
> ELE 103.69 11.46
> VDW -56.34 2.74
> INT 7.73 2.46
> GAS 55.08 10.76
> PBSUR -6.40 0.31
> PBCAL -41.62 11.08
> PBSOL -48.01 11.00
> PBELE 62.08 5.34
> PBTOT 7.06 4.49
> GBSUR -6.40 0.31
> GB -53.42 9.80
> GBSOL -59.82 9.75
> GBELE 50.27 3.57
> GBTOT -4.74 3.27
>
>
>
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>
--
T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
Graduate Student
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Sun Nov 14 2010 - 15:30:03 PST
