Hi,
Looks like some problem with you receptor information. It may be that
you have not correctly defined receptor and ligand molecules in the
input file.
Can you check that and try again.
Rafi
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of msubhamoy.ibab.ac.in
Sent: 14. august 2007 10:27
To: amber.scripps.edu
Subject: AMBER: MMPBSA NOT Getting results
Respected Sir
I am not getting the results for mmpbsa calculation. can any one help
me? I have
given both my input and output files.
This was my input file
>> Init data
Presuming executables of amber suite to be in
/home/gsmith/amber9/amber9/exe
=>> Reading input parameters
Found PREFIX => snapshot
Found PATH => ./
Found COMPLEX => 1
Found RECEPTOR => 1
Found LIGAND => 1
Found COMPT => ./comp_nowat.prmtop
Found RECPT => ./rec.prmtop
Found LIGPT => ./lig.prmtop
Found GC => 1
Found AS => 0
Found DC => 0
Found MM => 0
Found GB => 0
Found PB => 0
Found MS => 0
Found NM => 0
Found BOX => YES
Found NTOTAL => 24027
Found NSTART => 1
Found NSTOP => 4830
Found NFREQ => 1
Found NUMBER_LIG_GROUPS => 1
Found LSTART => 570
Found LSTOP => 1176
Found NUMBER_REC_GROUPS => 1
Found RSTART => 1
Found RSTOP => 569
Found TRAJECTORY => ./mdp1a.traj
Found TRAJECTORY => ./mdp1b.traj
Found TRAJECTORY => ./mdp1c.traj
Found TRAJECTORY => ./mdp1d.traj
Found TRAJECTORY => ./mdp1e.traj
=>> Checking sanity
Checking GENERAL
Checking GC
Checking TRAJ
=>> Creating input
make_crd input
=>> Creating coordinates
Executing makecrd
Amber8 Module: make_crg_hg
usage: make_crd_hg < trajectory_file
Box info found: 48.508 62.56 79.12
Box info found: 48.481 62.526 79.076
Box info found: 48.496 62.545 79.1
Box info found: 48.454 62.491 79.032
Box info found: 48.484 62.529 79.08
Box info found: 48.493 62.541 79.095
Box info found: 48.5 62.551 79.107
Box info found: 48.522 62.578 79.142
Box info found: 48.506 62.557 79.116
Box info found: 48.536 62.597 79.166
Box info found: 48.539 62.601 79.171
Box info found: 48.536 62.597 79.166
Box info found: 48.505 62.557 79.116
Box info found: 48.506 62.558 79.116
Box info found: 48.483 62.529 79.08
Box info found: 48.5 62.55 79.106
Box info found: 48.531 62.59 79.157
........
This was my output file ...
=>> Init data
Presuming executables of amber suite to be in
/home/gsmith/amber9/amber9/exe
=>> Reading input parameters
Found PREFIX => snapshot
Found PATH => ./
Found COMPLEX => 1
Found RECEPTOR => 1
Found LIGAND => 1
Found COMPT => ./comp_nowat.prmtop
Found RECPT => ./rec.prmtop
Found LIGPT => ./lig.prmtop
Found GC => 0
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 => 1.4
Found ISTRNG => 0.0
Found RADIOPT => 0
Found NPOPT => 1
Found CAVITY_SURFTEN => 0.0072
Found CAVITY_OFFSET => 0.00
Found SURFTEN => 0.0072
Found SURFOFF => 0.00
Found DIELC => 1.0
Found IGB => 2
1,0-1
Top
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 => 0.0
=>> Checking sanity
Checking GENERAL
Checking MM
Checking PB
Checking GB
Checking MS
=>> Creating input
Sander input
PBSA input
=>> Calculating energy / entropy contributions
Calc contrib for ./snapshot_com.crd.1
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for ./snapshot_com.crd.2
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for ./snapshot_com.crd.3
72,5
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for ./snapshot_com.crd.4
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for ./snapshot_com.crd.5
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for ./snapshot_com.crd.6
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for ./snapshot_com.crd.7
Calc MM/GB/SAS
........................... it countinued till
Calc contrib for ./snapshot_com.crd.4830
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
Calc MS
Calc contrib for ./snapshot_rec.crd.1
Calc MM/GB/SAS
it stopped here... wat happened ... i didnot understand....
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Received on Wed Aug 15 2007 - 06:07:42 PDT
