Re: Re: [AMBER] problem in MMPBSA

From: Dima A Sabbah <dsabbah.unmc.edu>
Date: Sun, 18 Apr 2010 13:52:55 -0500

    1. look at MM array and PB array.
    2. search for EPB and ELRA= FE using / command in terminal

   --= ---amber-bounces.ambermd.org wrote: -----

     To: "AMBER Mailing List" <amber.amb= ermd.org>
     From: "zgong.hust" <zgong.hust.gmail.com>
     Sent by:= amber-bounces.ambermd.org
     Date: 04/17/2010 08:49PM
     Subject: Re: Re: = [AMBER] problem in MMPBSA
     Dear sir:
            I fol= lowed you advise to edit the mm_pbsa_statistics.pm,
     however, in my mm= _pbsa_statistics.pm file, there no ELRAELE, EPB and
     NONPOL, I have used= the AMBER 9, what's wrong with it ?
     Thank you
     2010-04-18 Zhou Gong
     School of Physics
     Huazhong University of S= cience and Technology
     Wuhan
     Hubei Province
     China
     &#= 21457;件人š Dima A Sabbah
     ‘€—&#= 38388;š 2010-04-18 01:09:48
     ”件人‚= 6; AMBER Mailing List
     Š„€š
     主˜A= 306; Re: [AMBER] problem in MMPBSA

        Hi Zhong,
     = I encountered the same problem and I solved = i= t. Please
     follow the
        following steps:
        = 1. cd $AMBERHOME
         2. cd= src
        &= nbsp;3. cp mm_pbsa to your home (I typed in terminal :cp -rf
     mm_pb= s= a
            /home/Dima)
         4. cp mm= _pbsa_statistics.pm mm_pbsa= _statistics.pm_old
      = 5. vim mm_pbsa_statistics.pm
         6= . edit ELRAELE => [1.0 to 0.0
         7. edit EPB = => [= 1.0 to 0.0
         8. edit PBNONPOL => [1.0= to 0.0
         9. save = ; mm_pbsa_statistics.pm
     &n= bsp; 10. Go to your working directory &nb= sp; and t=
     ype (I typed
         = ; /home/Dima/mm_pbsa/mm_pbsa.pl ./input mm_pbsa.in
     &n= bsp; 11. I faced a new problem no data for MM + 0 , I edi= tted
     also GB &n bsp;=> [1.0 to 0.0
     &= nbsp; The Best of Luck!
        &nbs= p;
       = ; -----amber-bounces.ambe= rmd.org wrote: -----
          To= : "AMBER Mailing List" <amber.ambermd.org>
          Fro= m: "= zgong.hust" <zgong.hust.gmail.com>
          Sen= t by: amber-bounces.ambermd.= org
          Date: 04/17/2010= 10:06AM
          Subject: [AMBER] problem in MMPBSA
      = ; H= i, all,
          When I calculate the bin= ding energy of RNA-small molecule i=
     nteraction by
         = MM_PBSA in AMBER9. Input file is as following:
          PR= EF= IX snapshot
          PATH = &nb= sp; ./
          #
          CO= M= PLEX 1
        &nb= sp; RECEPTOR = 1
      = LIGAND = &= nbsp; 1
          #
          COMPT = &nbs= p; ./1y26_a.prmtop RECPT &nbs=
     p; &nbs= p; ./1y26.prmtop
          LIGPT = &nbs= p; ./a.prmtop
        &nb= sp; #
          GC &nb= sp; = 0
          AS &= nbsp= ; 0
      = DC= = 0
          = #
          MM &nbs= p; 1 GB &nbs= p; 1 P= B
                        = = ;1
          MS &nbs= p; 1#
          NM &= nbsp; 0<= BR>#
          # PROC &nbs= p; 2 REFE &n= bsp; 0
          INDI = 1.0
          EXDI = 80.0
       = SCALE 2
     &= nbsp; LINIT &n= bsp; = 1000
          PRBRAD = &n= bsp; 1.4
          ISTRNG &= amp;nbs= p; 0.0
          RADIOP= T &= nbsp; 0
       = ; NPOPT &n= bsp; &nb= sp; 1
          CAVITY_SURFTEN 0.= 0072
          CAVI= TY_OFFSET = 0.00
          #
          SURFTEN = = 0.0072
          SURFO= FF &= nbsp; 0.00
      &= nbsp; #
          IGB &= nb= sp; 2
          GBSA = = ; 1
     &nb= sp; SALTCON = ; &nb= sp; 0.00
          EXTDIEL = &= nbsp; 80.0
          INTDIEL &nbs= p; = ; 1.0
         = ; #
          SURFTEN &= nbs= p; 0.0072
          SURFOFF = = ; 0.00
          when I run th= e mm_pbsa.pl, it shows
          Use of uninit= ial= ized value in multiplication (*)
     &= nbsp;at
                           /export/home/gz/soft/amber9/src/mm_pb=sa /mm_pbsa_statistics.pm
          line 1336.
       = ; Use of uninitialized value in m= u= ltiplication
     (*) at
          /export/ home/gz/soft/amber9/src/mm_pbsa/mm_pbsa_s=tatistics.pm
      &nb= sp; line 1336.
              No data for 0+2 = PB PB 0
          the output file are like this :
      &nb= sp; MM
          GB
          PB
      = MS
          1
           = = ;BOND = 617.4072 ANGLE = = = 1269.1704
     DIHED =
      &n= bsp; 1= 818.2919
            VDWAAL= S = -1366.1237 EEL &nbs= p; = &n= bsp;
     32178.2971 EGB
          = &nb= sp; -= 41925.7449
           1-4 VDW = 639= .5718 1-4= EEL = -6010.0127 RESTRAINT
      = =
          &n= bsp; 0.0000
        &nbs= p; corrected reaction field energy: -71281.229816<= BR>surfa ce area =
          12031.916
          ECAVITY= = 12031.916
          EDISP= ER = 0.0000
      = ; 2
           BOND = = 579.3= 947 ANGLE = 1293.0841 &n bsp;DIHED = ; =
             = 1823.4181
           VDWAALS = -1342= .= 5240 EEL = 32086.1669 EGB = =
            -41862.3644
     &n= bsp; 1-4 VDW = &nbs= p; 644.4107 &n= bsp;1-4 EEL =
     -5959.7021 RESTRAINT = &= nbsp; 0.0000
          corrected reaction = field en= ergy: -71145.860423
          surface area = = 12105.554
          ECAVITY = = 12105.554<= BR> EDISPER = 0.0000
          there are = no statistics fi= le
          How can I fix this ?
      = ; Thank you
          2010-04-16
        = Zhou Gong
          School of Physi= cs
          Huazhong University of Science an= d Technology Wuhan
          Hubei Province
     &nbs= p; China
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References

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Received on Sun Apr 18 2010 - 12:00:02 PDT
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