AMBER Archive (2007)

Subject: AMBER: MMPBSA NOT Getting results

From: msubhamoy_at_ibab.ac.in
Date: Tue Aug 14 2007 - 03:26:57 CDT


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_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu