AMBER Archive (2006)

Subject: AMBER: MM_PBSA problem (No values for MM_GAS )

From: Bing Liu (bliu999_at_yahoo.com)
Date: Mon Feb 13 2006 - 08:40:47 CST


Dear Amber users,
   
    I try to calculate the binding energy using both GB and PB models of amber8 mm-pbsa program. My calculation stopped at ¡®=>> Calc delta from raw data¡¯ and gave some wrong information such as ¡®No values for MM_GAS existing -> Skipping¡¯. The mm_pbsa.in and mm_pbsa.out file are listed as follow. I highly appreciate ones who have the similar experience and can give me some advice.
    Thanks in advance!
   
  Bing Liu
   
   
  mm_pbsa.in
   
  #
  # Input parameters for mm_pbsa.pl
  #
  # Holger Gohlke
  # 08.02.2002
  #
  ################################################################################
  @GENERAL
  #
  PREFIX DHPL-KES
  PATH ./
  #
  COMPLEX 1
  RECEPTOR 1
  LIGAND 1
  #
  COMPT ./complex.top
  RECPT ./receptor.top
  LIGPT ./ligand.top
  #
  GC 1
  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
  SCALE 2
  LINIT 1000
  PRBRAD 1.6
  #
  RADIOPT 0
  #
  FOCUS 0
  PERFIL 80.0
  CHARGE /home/program/amber8/src/mm_pbsa/Examples/my_amber94_delphi.crg
  SIZE /home/program/amber8/src/mm_pbsa/Examples/my_parse_delphi.siz
  #
  SURFTEN 0.00542
  SURFOFF 0.092
  #
  #
  ################################################################################
  @MM
  #
  #
  DIELC 1.0
  #
  ################################################################################
  @GB
  #
  IGB 1
  GBSA 1
  SALTCON 0.00
  EXTDIEL 80.0
  INTDIEL 1.0
  #
  SURFTEN 0.0072
  SURFOFF 0.00
  #
  ################################################################################
  @MS
  #
  PROBE 1.4
  #
  ##################################################################################
  @NM
  #
  DIELC 4
  MAXCYC 10000
  DRMS 0.0001
  #
  #################################################################################
  @MAKECRD
  #
  BOX NO
  NTOTAL 4135
  NSTART 1
  NSTOP 200
  NFREQ 100
  #
  NUMBER_LIG_GROUPS 1
  LSTART 4105
  LSTOP 4135
  NUMBER_REC_GROUPS 1
  RSTART 1
  RSTOP 4104
  #
  #################################################################################
  @TRAJECTORY
  #
  TRAJECTORY ../DHPL-KES.md_stripped.xx
  #
  ###############################################################################
  @PROGRAMS
  #
  DELPHI /home/program/delphi/delphi
    #

   
   
  mm_pbsa.out
   
   
  =>> Init data
      Presuming executables of amber suite to be in /home/program/amber8/exe
   
  =>> Reading input parameters
      Found PREFIX => DHPL-KES
      Found PATH => ./
      Found COMPLEX => 1
      Found RECEPTOR => 1
      Found LIGAND => 1
      Found COMPT => ./complex.top
      Found RECPT => ./receptor.top
      Found LIGPT => ./ligand.top
      Found GC => 1
      Found AS => 0
      Found DC => 0
      Found MM => 1
      Found GB => 1
      Found PB => 1
      Found MS => 1
      Found NM => 0
      Found PROC => 2
      Found REFE => 0
      Found INDI => 1.0
      Found EXDI => 80.0
      Found SCALE => 2
      Found LINIT => 1000
      Found PRBRAD => 1.6
      Found RADIOPT => 0
      Found FOCUS => 0
      Found PERFIL => 80.0
      Found CHARGE => /home/program/amber8/src/mm_pbsa/Examples/my_amber94_delphi.crg
      Found SIZE => /home/program/amber8/src/mm_pbsa/Examples/my_parse_delphi.siz
      Found SURFTEN => 0.00542
      Found SURFOFF => 0.092
      Found DIELC => 1.0
      Found IGB => 1
      Found GBSA => 1
      Found SALTCON => 0.00
      Found EXTDIEL => 80.0
      Found INTDIEL => 1.0
      Found SURFTEN => 0.0072
      Found SURFOFF => 0.00
      Found PROBE => 1.4
      Found RADII => ./atmtypenumbers
      Found DIELC => 4
      Found MAXCYC => 10000
      Found DRMS => 0.0001
      Found BOX => NO
      Found NTOTAL => 4135
      Found NSTART => 1
      Found NSTOP => 200
      Found NFREQ => 100
      Found NUMBER_LIG_GROUPS => 1
      Found LSTART => 4105
      Found LSTOP => 4135
      Found NUMBER_REC_GROUPS => 1
      Found RSTART => 1
      Found RSTOP => 4104
      Found TRAJECTORY => ../DHPL-KES.md_stripped.xx
      Found DELPHI => /home/program/delphi/delphi
   
  =>> Checking sanity
      Checking GENERAL
      Checking GC
      Checking TRAJ
      Checking MM
      Checking PB
      Checking GB
      Checking MS
   
  =>> Creating input
      Sander input
      PBSA input
      make_crd input
   
  =>> Creating coordinates
      Executing makecrd
    
   Amber8 Module: make_crg_hg
    
   usage: make_crd_hg < trajectory_file
    
   
  =>> Calculating energy / entropy contributions
      Calc contrib for ./DHPL-KES_com.crd.1
          Calc MM/GB/SAS
          Generate PDB
          Center PDB
          Calc PBSA
          Generate PQR
          Calc MS
      Calc contrib for ./DHPL-KES_com.crd.2
          Calc MM/GB/SAS
          Generate PDB
          Center PDB
          Calc PBSA
          Generate PQR
          Calc MS
      Calc contrib for ./DHPL-KES_rec.crd.1
          Calc MM/GB/SAS
          Generate PDB
          Center PDB
          Calc PBSA
          Generate PQR
          Calc MS
      Calc contrib for ./DHPL-KES_rec.crd.2
          Calc MM/GB/SAS
          Generate PDB
          Center PDB
          Calc PBSA
          Generate PQR
          Calc MS
      Calc contrib for ./DHPL-KES_lig.crd.1
          Calc MM/GB/SAS
          Generate PDB
          Center PDB
          Calc PBSA
          Generate PQR
          Calc MS
      Calc contrib for ./DHPL-KES_lig.crd.2
          Calc MM/GB/SAS
          Generate PDB
          Center PDB
          Calc PBSA
          Generate PQR
          Calc MS
   
  =>> Doing statistics
  =>> Values of global variables
      TEMP = 300
      R = 8.314
      gammaP = 0.00542
      betaP = 0.092
      gammaG = 0.0072
      betaG = 0.00
  =>> Reading input
  =>> Reordering files
      Final order:
      1. DHPL-KES_com.all.out: -
      2. DHPL-KES_rec.all.out: -
      3. DHPL-KES_lig.all.out: -
  =>> Reading files
      Reading DHPL-KES_com.all.out
      WARNING: Missing SURF for MS in 0 -> Taken from -1
      WARNING: Missing SURF for MS in 1 -> Taken from 0
      Reading DHPL-KES_rec.all.out
      Checking CALC
      WARNING: Missing SURF for MS in 0 -> Taken from -1
      WARNING: Missing SURF for MS in 1 -> Taken from 0
      Reading DHPL-KES_lig.all.out
      Checking CALC
  =>> Treat special parameters
  =>> Calc missing parameters
      Processing MM ELE
          Doing 1 MM ELENB
          Doing 1 MM ELE14
          Doing 1 MM ELENB
          Doing 1 MM ELE14
          Doing 1 MM ELENB
          Doing 1 MM ELE14
      Processing MM GAS
          Doing 1 MM ELE
          Doing 1 MM VDW
      No values for MM_VDW existing -> Skipping
      Processing MM INT
          Doing 1 MM BOND
          Doing 1 MM ANGLE
          Doing 1 MM DIHED
          Doing 1 MM BOND
          Doing 1 MM ANGLE
          Doing 1 MM DIHED
          Doing 1 MM BOND
          Doing 1 MM ANGLE
          Doing 1 MM DIHED
      Processing MM VDW
          Doing 1 MM VDWNB
          Doing 1 MM VDW14
          Doing 1 MM VDWNB
          Doing 1 MM VDW14
          Doing 1 MM VDWNB
          Doing 1 MM VDW14
      Processing GB GBTOT
          Doing 1 GB GBSOL
      No values for GB_GBSOL existing -> Skipping
      Processing GB GBELE
          Doing 1 GB GB
          Doing 1 MM ELE
          Doing 1 GB GB
          Doing 1 MM ELE
          Doing 1 GB GB
          Doing 1 MM ELE
      Processing GB GBSOL
          Doing 1 GB GB
          Doing 1 GB GBSUR
          Doing 1 GB GB
          Doing 1 GB GBSUR
          Doing 1 GB GB
          Doing 1 GB GBSUR
      Processing PB PBSOL
          Doing 1 PB PBCAL
          Doing 1 PB PBSUR
          Doing 1 PB PBCAL
          Doing 1 PB PBSUR
          Doing 1 PB PBCAL
          Doing 1 PB PBSUR
      Processing PB PBELE
          Doing 1 PB PBCAL
          Doing 1 MM ELE
          Doing 1 PB PBCAL
          Doing 1 MM ELE
          Doing 1 PB PBCAL
          Doing 1 MM ELE
      Processing PB PBTOT
          Doing 1 PB PBSOL
          Doing 1 MM GAS
      No values for MM_GAS existing -> Skipping
      Processing MM GAS
          Doing 1 MM ELE
          Doing 1 MM VDW
          Doing 1 MM INT
          Doing 1 MM ELE
          Doing 1 MM VDW
          Doing 1 MM INT
          Doing 1 MM ELE
          Doing 1 MM VDW
          Doing 1 MM INT
      Processing GB GBTOT
          Doing 1 GB GBSOL
          Doing 1 MM GAS
          Doing 1 GB GBSOL
          Doing 1 MM GAS
          Doing 1 GB GBSOL
          Doing 1 MM GAS
      Processing PB PBTOT
          Doing 1 PB PBSOL
          Doing 1 MM GAS
          Doing 1 PB PBSOL
          Doing 1 MM GAS
          Doing 1 PB PBSOL
          Doing 1 MM GAS
  =>> Calc delta from raw data

                
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