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....
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Aug 15 2007 - 06:07:41 PDT
