AMBER Archive (2007)

Subject: RE: AMBER: MMPBSA NOT Getting results

From: Rafi Ahmad (Rafi.Ahmad_at_fagmed.uit.no)
Date: Tue Aug 14 2007 - 03:34:35 CDT


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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of msubhamoy_at_ibab.ac.in
Sent: 14. august 2007 10:27
To: amber_at_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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