I just found the reason:
In MD run, I forgot to add the S-S bond.
In the pbsa run, I added the S-S bond.
Thank all
I'll re-run it. Thanks again!
2010/12/6 Alice Wang <compu.chem.w.gmail.com>
> snap:
> #Generate snapshots
> .GENERAL
> PREFIX snapshot
> PATH ./
> #
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> #
> COMPT ../com.top
> RECPT ../rec.top
> LIGPT ../lig.top
> #
> GC 1
> AS 0
> DC 0
> #
> MM 0
> GB 0
> PB 0
> MS 0
> #
> NM 0
> #
> .MAKECRD
> BOX YES
> NTOTAL 47015
> NSTART 1
> NSTOP 1000
> NFREQ 10
> #
> NUMBER_LIG_GROUPS 1
> LSTART 6707
> LSTOP 6733
> NUMBER_REC_GROUPS 1
> RSTART 1
> RSTOP 6706
> #
> .TRAJECTORY
> TRAJECTORY ../../rst/md1.rst
>
> ------------------------------------------------------------
> bind:
> .GENERAL
> PREFIX snapshot
> PATH ../snap1/
> #
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> #
> COMPT ../com.top
> RECPT ../rec.top
> LIGPT ../lig.top
> #
> GC 0
> AS 0
> DC 0
> #
> MM 1
> GB 0
> PB 1
> MS 1
> #
> NM 0
> #
> .PB
> PROC 2
> REFE 0
> INDI 1.0
> EXDI 80.0
> SCALE 3
> LINIT 1000
> 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
> #
> .MS
> PROBE 0.0
> -----------------------------------------------------
> snapshot_com.all.out :
> MM
> PB
> MS
> PB_SURFTEN 0.0072
> PB_SURFOFF 0.00
> 1
> BOND = 5527.7282 ANGLE = 3549.8797 DIHED =
> 4572.4897
> VDWAALS = -3299.2570 EEL = -24133.5090 HBOND =
> 0.0000
> 1-4 VDW = 1522.5552 1-4 EEL = 17390.0677 RESTRAINT =
> 0.0000
> corrected reaction field energy: -14225.509919
> surface area = 21291.846
> ECAVITY = 21291.846
> EDISPER = 0.0000
> 2
> BOND = 5611.7242 ANGLE = 3540.7968 DIHED =
> 4619.9158
> VDWAALS = -3305.0051 EEL = -24225.6943 HBOND =
> 0.0000
> 1-4 VDW = 1535.7690 1-4 EEL = 17352.0963 RESTRAINT =
> 0.0000
> corrected reaction field energy: -14156.988741
> surface area = 21545.567
> ECAVITY = 21545.567
> EDISPER = 0.0000
> 3
> BOND = 4998.5208 ANGLE = 3531.3218 DIHED =
> 4624.3629
> VDWAALS = -3291.2172 EEL = -24219.7381 HBOND =
> 0.0000
> 1-4 VDW = 1542.0590 1-4 EEL = 17392.9788 RESTRAINT =
> 0.0000
> corrected reaction field energy: -14234.833418
> surface area = 21916.489
> ECAVITY = 21916.489
> EDISPER = 0.0000
> 4
> BOND = 6991.5351 ANGLE = 3641.5053 DIHED =
> 4572.9531
> VDWAALS = -3296.2592 EEL = -24393.0952 HBOND =
> 0.0000
> 1-4 VDW = 1519.4070 1-4 EEL = 17410.9097 RESTRAINT =
> 0.0000
> corrected reaction field energy: -13952.250701
> surface area = 21664.640
> ECAVITY = 21664.640
> EDISPER = 0.0000
> 5
> BOND = 6940.7391 ANGLE = 3642.5870 DIHED =
> 4564.7746
> VDWAALS = -3299.1843 EEL = -24230.0725 HBOND =
> 0.0000
> 1-4 VDW = 1538.1436 1-4 EEL = 17368.4994 RESTRAINT =
> 0.0000
> corrected reaction field energy: -14053.602574
> surface area = 21557.437
> ECAVITY = 21557.437
> EDISPER = 0.0000
> 6
> BOND = 7215.2873 ANGLE = 3672.7766 DIHED =
> 4568.3137
> VDWAALS = -3314.8553 EEL = -24275.1713 HBOND =
> 0.0000
> 1-4 VDW = 1555.6592 1-4 EEL = 17391.5978 RESTRAINT =
> 0.0000
> corrected reaction field energy: -13898.868551
> surface area = 21627.317
> ECAVITY = 21627.317
> EDISPER = 0.0000
> 7
> BOND = 6904.6747 ANGLE = 3632.9319 DIHED =
> 4570.6171
> VDWAALS = -3295.2435 EEL = -24241.0596 HBOND =
> 0.0000
> 1-4 VDW = 1524.1689 1-4 EEL = 17403.3138 RESTRAINT =
> 0.0000
> corrected reaction field energy: -14012.598300
> surface area = 21864.893
> ECAVITY = 21864.893
> EDISPER = 0.0000
> 8
> BOND = 6572.0523 ANGLE = 3666.1718 DIHED =
> 4578.6093
> VDWAALS = -3290.7906 EEL = -24347.6482 HBOND =
> 0.0000
> 1-4 VDW = 1513.1670 1-4 EEL = 17378.5779 RESTRAINT =
> 0.0000
> corrected reaction field energy: -13954.055682
> surface area = 21868.032
> ECAVITY = 21868.032
>
> -------------------------------------------------------------
> amber10 with mm_pbsa.pl
>
> I found the "BOND" in sanpshot_com.all.out file varied greatly....from 5000
> to 10000....
>
>
> 2010/12/6 Ray Luo, Ph.D. <ray.luo.uci.edu>
>
> Can you share with us your mmpba input file and which version of amber you
>> are using?
>>
>> Ray
>>
>> On Sun, Dec 5, 2010 at 7:12 PM, Alice Wang <compu.chem.w.gmail.com>
>> wrote:
>>
>> > Thank you Jason
>> > I checked the *out file, the number is ok
>> > but when I check the mm_pbsa.log, I found the warning, as blew, is it
>> the
>> > reason? how to solve it ? Thanks it again.
>> >
>> > =>> Reordering files
>> > Final order:
>> > 1. snapshot_com.all.out: -
>> > 2. snapshot_rec.all.out: -
>> > 3. snapshot_lig.all.out: -
>> > =>> Reading files
>> > Reading snapshot_com.all.out
>> > WARNING: Missing PBCAV for PB in 88 -> Taken from 87
>> > WARNING: Missing PBDIS for PB in 88 -> Taken from 87
>> > WARNING: Missing SURF for MS in 88 -> Taken from 87
>> > Reading snapshot_rec.all.out
>> > Checking consistency of CALC
>> > Checking consistency of DATA
>> > Reading snapshot_lig.all.out
>> > Checking consistency of CALC
>> > Checking consistency of DATA
>> >
>> >
>> >
>> > 2010/12/6 Jason Swails <jason.swails.gmail.com>
>> >
>> > > Look at the temporary output files created by sander and see if the
>> > numbers
>> > > make sense. Depending on the version of mm_pbsa that you're using,
>> > either
>> > > pbsa_com.#.out, pbsa_rec.#.out, pbsa_lig.#.out (for amber10/amber11, I
>> > > think) and sander_com.#.out, etc.
>> > >
>> > > Make sure you set VERBOSE to a proper setting so that it keeps all of
>> the
>> > > files. See the amber manual for a more detailed discussion.
>> > >
>> > > All the best,
>> > > Jason
>> > >
>> > > On Sun, Dec 5, 2010 at 9:26 PM, Alice Wang <compu.chem.w.gmail.com>
>> > wrote:
>> > >
>> > > > Dear Amber,
>> > > >
>> > > > My pbsa out put file is blow:
>> > > > # COMPLEX RECEPTOR
>> > > > LIGAND
>> > > > # ----------------------- -----------------------
>> > > > -----------------------
>> > > > # MEAN STD MEAN STD
>> > > > MEAN STD
>> > > > # ======================= =======================
>> > > > =======================
>> > > > ELE -6803.94 114.19 -6670.34 114.97
>> > > > -101.61 1.59
>> > > > VDW -1772.99 26.24 -1734.65 26.33
>> > > > 5.04 1.38
>> > > > INT 16439.74 2118.23 16405.28 2118.61
>> > > > 34.47 3.69
>> > > > GAS 7862.82 2103.51 8000.29 2101.62
>> > > > -62.10 3.76
>> > > > PBSUR 157.30 1.27 158.36 1.29
>> > > > 3.21 0.02
>> > > > PBCAL -8491.30 115.80 -8517.82 116.78
>> > > > -20.24 1.30
>> > > > PBSOL -8333.99 115.33 -8359.46 116.33
>> > > > -17.03 1.30
>> > > > PBELE -15295.23 43.75 -15188.16 43.63
>> > > > -121.85 1.32
>> > > > PBTOT -471.17 2106.88 -359.17 2106.46
>> > > > -79.13 3.67
>> > > >
>> > > > # DELTA
>> > > > # -----------------------
>> > > > # MEAN STD
>> > > > # =======================
>> > > > ELE -31.99 3.11
>> > > > VDW -43.38 2.20
>> > > > INT -0.00 0.00
>> > > > GAS -75.37 3.88
>> > > > PBSUR -4.26 0.21
>> > > > PBCAL 46.76 3.32
>> > > > PBSOL 42.50 3.36
>> > > > PBELE 14.77 2.58
>> > > > PBTOT -32.87 3.02
>> > > >
>> > > > The STD value is high in the PBTOT of complex, receptor.
>> > > >
>> > > > Is it wrong?
>> > > >
>> > > > Thanks !
>> > > >
>> > > > Alice Wang
>> > > > _______________________________________________
>> > > > AMBER mailing list
>> > > > AMBER.ambermd.org
>> > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > >
>> > >
>> > >
>> > >
>> > > --
>> > > Jason M. Swails
>> > > Quantum Theory Project,
>> > > University of Florida
>> > > Ph.D. Graduate Student
>> > > 352-392-4032
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> _______________________________________________
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>>
>
>
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Received on Mon Dec 06 2010 - 00:00:04 PST
