Re: Re: [AMBER] problem in MMPBSA

From: zgong.hust <zgong.hust.gmail.com>
Date: Sun, 18 Apr 2010 09:49:01 +0800

Dear sir:
       I followed 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 Science and Technology
Wuhan
Hubei Province
China



发件人: Dima A Sabbah
发送时间: 2010-04-18 01:09:48
收件人: AMBER Mailing List
抄送:
主题: 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
    3. cp mm_pbsa to your home (I typed in terminal :cp -rf mm_pb= sa
       /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
   10. Go to your working directory and t= ype (I typed
       /home/Dima/mm_pbsa/mm_pbsa.pl ./input mm_pbsa.in
   11. I faced a new problem no data for MM + 0 , I editted also GB &n bsp;=> [1.0 to 0.0
   The Best of Luck!
   &nbs= p;
   -----amber-bounces.ambe= rmd.org wrote: -----
     To: "AMBER Mailing List" <amber.ambermd.org>
     From: "= zgong.hust" <zgong.hust.gmail.com>
     Sent by: amber-bounces.ambermd.= org
     Date: 04/17/2010 10:06AM
     Subject: [AMBER] problem in MMPBSA
     H= i, all,
     When I calculate the binding energy of RNA-small molecule i= nteraction by
     MM_PBSA in AMBER9. Input file is as following:
     PREF= IX snapshot
     PATH = ./
     #
     CO= MPLEX 1
     RECEPTOR = 1
     LIGAND = 1
     #
     COMPT &nbs= p; ./1y26_a.prmtop
     RECPT &nbs= p; ./1y26.prmtop
     LIGPT = ./a.prmtop
     #
     GC &nb= sp; 0
     AS &= nbsp; 0
     DC= 0
     = #
     MM 1 GB 1 PB = ;1
     MS 1#
     NM 0<= BR>#
     #
     PROC 2 REFE 0
     INDI 1.0
     EXDI 80.0
     SCALE 2
     LINIT &n= bsp; 1000
     PRBRAD = 1.4
     ISTRNG &nbs= p; 0.0
     RADIOPT &= nbsp; 0
     NPOPT &n= bsp; 1
     CAVITY_SURFTEN 0.0072
     CAVI= TY_OFFSET 0.00
     #
     SURFTEN = 0.0072
     SURFOFF &= nbsp; 0.00
     #
     IGB &nb= sp; 2
     GBSA = ; 1
     SALTCON = ; 0.00
     EXTDIEL &= nbsp; 80.0
     INTDIEL = ; 1.0
     #
     SURFTEN &nbs= p; 0.0072
     SURFOFF = ; 0.00
     when I run the mm_pbsa.pl, it shows
     Use of uninitial= ized value in multiplication (*) at
     /export/home/gz/soft/amber9/src/mm_pb=sa/mm_pbsa_statistics.pm
     line 1336.
     Use of uninitialized value in mu= ltiplication (*) at
     /export/home/gz/soft/amber9/src/mm_pbsa/mm_pbsa_s=tatistics.pm
     line 1336.
         No data for 0+2 PB PB 0
     the output file are like this :
     MM
     GB
     PB
     MS
     1
      = ;BOND = 617.4072 ANGLE = = 1269.1704 DIHED =
         1= 818.2919
      VDWAALS = -1366.1237 EEL &nbs= p; = 32178.2971 EGB
     = &nb= sp; -41925.7449
      1-4 VDW = 639.5718 1-4= EEL = -6010.0127 RESTRAINT =
     &n= bsp; 0.0000
     corrected reaction field energy: -71281.229816<= BR>surface area =
     12031.916
     ECAVITY = 12031.916
     EDISP= ER = 0.0000
     2
      BOND = 579.3= 947 ANGLE = 1293.0841 DIHED = ; =
         1823.4181
      VDWAALS = -1342= .5240 EEL = 32086.1669 EGB = =
       -41862.3644
      1-4 VDW = &nbs= p; 644.4107 1-4 EEL = -5959.7021 RESTRAINT = 0.0000
     corrected reaction field en= ergy: -71145.860423
     surface area = 12105.554
     ECAVITY = = 12105.554
     EDISPER = 0.0000
     there are no statistics fi= le
     How can I fix this ?
     Thank you
     2010-04-16
          Zhou Gong
     School of Physics
     Huazhong University of Science an= d Technology
     Wuhan
     Hubei Province
     China
     _______ ________________________ 5F= _______________
     AMBER mailing list
     AMBE= R.ambermd.org
     [1]http://lists.ambermd.org/mailman/listinfo/amber
     
   
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Received on Sat Apr 17 2010 - 19:00:02 PDT
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