Dear mukherjee,
I think i had been found the same problem as you but what i check is that
the number of atoms in the topology file corresponding to the REC, LIG and
COM files are same ?. If not, that should cause this errors.
Best regards,
Jitrayut
Department of Chemistry,
Faculty of Science,
Chiang Mai University,
Thailand
2007/8/21, msubhamoy.ibab.ac.in <msubhamoy.ibab.ac.in>:
>
> Respected Sir
> I have tried a lot. but my mmpbsa program is stopping here. There is no
> problem
> with the receptor file.
> I have checked. Please help me out .
>
>
>
> S.mukherjee
>
>
>
> =>> 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
>
> 24,5
>
>
>
>
>
>
>
>
>
>
> 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
> 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
> Calc MM/GB/SAS
> Generate PDB
> Center PDB
> Calc PBSA
> Generate PQR
> ........ it continued till
> Calc contrib for ./snapshot_com.crd.4830
> Calc MM/GB/SAS
> Generate PDB
> Center PDB
> Calc PBSA
> Generate PQR
> Calc MS
> then it gave
>
> Calc contrib for ./snapshot_rec.crd.1
> Calc MM/GB/SAS
> there is no problem with the receptor file..... then why is the program
> stopping?
>
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Received on Wed Aug 22 2007 - 06:07:33 PDT
