Glad you found it ...
Good luck with your project!
Ray
==========================================
Ray Luo, Ph.D.
Associate Professor in Computational
Biochemistry and Molecular Biophysics
Dept of Molecular Biology and Biochemistry
Dept of Biomedical Engineering
University of California, Irvine, CA 92697-3900
Email: rluo.uci.edu Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/rayl/
==========================================
On 12/5/2010 11:48 PM, Alice Wang wrote:
> 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
>>>>>
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>>>>
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
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Received on Mon Dec 06 2010 - 10:30:02 PST
