Bing,
This looks like it is a problem with your coordinate file definitions. Try
to create a pdb file with one of your coordinate file and the unsolvated
parmtop file (ambpdb -p parmtop <coordinate> pdbfile). Look at the pdb
structure and see if it looks normal. More than likely, you have not
stripped out waters and ions out of the coordinate file.
Scott
On 2/13/06, Bing Liu <bliu999.yahoo.com> wrote:
>
> 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 ¡(r)=>> Calc delta from raw
> data¡¯ and gave some wrong information such as ¡(r)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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Received on Sun Feb 19 2006 - 06:10:09 PST
