Try using MMPBSA.py instead (built alongside AmberTools 1.5). It has better
error catching, and may help you find out what's happening.
HTH,
Jason
2011/5/8 Andrew Voronkov <drugdesign.yandex.ru>
> What confuses me is that there is the difference in number of atoms between
> coordinates atoms from snapshots, but no difference with coordinates in rst
> file resulted from molecular dynamics from mdrcd trajectory. So something is
> wrong with parametrization of protein-ligand complex without solvent, some
> difference of it with number of atoms in the sanpshots.
>
> [voronkov.t60-2 36739]$ $AMBERHOME/exe/ambpdb -p 36739now.prmtop
> <snapshot_com.crd.1> 36739-min1.pdb
> | New format PARM file being parsed.
> | Version = 1.000 Date = 05/08/11 Time = 14:47:26
>
> ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 3911 3862
> COULD NOT READ COORDINATES FROM RESTRT FILE
> [voronkov.t60-2 36739]$ $AMBERHOME/exe/ambpdb -p 36739.prmtop
> <36739_md1.rst> 36739_md1.pdb
> | New format PARM file being parsed.
> | Version = 1.000 Date = 01/28/10 Time = 16:41:20
> [voronkov.t60-2 36739]$
>
> Best regards,
> Andrew
>
> 08.05.2011, 17:57, "Andrew Voronkov" <drugdesign.yandex.ru>:
> >>> sander -O -i sander_com.in -o sander_com.1.out -c
> ./snapshot_com.crd.1 -p
> >>> ./39981.prmtop not successful
> >
> > - this was error from mmpbsa_energy script run, i ve tested first
> snapshot with ambpdb andgot problem about prmtop file and crd file
> coordinates mismatch.
> >
> > The problem turned out to be with crd and prmtop files
> >
> > [voronkov.t60-2 34139]$ $AMBERHOME/exe/ambpdb -p 34139now.prmtop
> <snapshot_com.crd.1> snapshot_com.pdb
> > | New format PARM file being parsed.
> > | Version = 1.000 Date = 05/08/11 Time = 14:45:17
> >
> > ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 3908 3862
> > COULD NOT READ COORDINATES FROM RESTRT FILE
> >
> > now have to resolve what additional atoms I have in prmtop file.
> >
> > 07.05.2011, 22:54, "Jason Swails" <jason.swails.gmail.com>;:
> >
> >> 2011/5/7 Andrew Voronkov <drugdesign.yandex.ru>;;
> >>> Yes, sure, just copied wrong line, but anyway with that line seems
> like
> >>> there is no problems, nothing is reported. But I get an error it when
> run
> >>> mmpbsa_energy.pl script:
> >>>
> >>> sander -O -i sander_com.in -o sander_com.1.out -c
> ./snapshot_com.crd.1 -p
> >>> ./39981.prmtop not successful
> >> It appears as though this is the full command you're trying to enter.
> Thus,
> >> it is parsing "not" as a flag, which it doesn't recognize. Take out
> "not
> >> successful" and rerun it.
> >>> here is the log, looks normal:
> >>>
> >>> =>> Init data
> >>> Presuming executables of amber suite to be in
> >>> /home/osolodkin/amber10/exe
> >>>
> >>> =>> Reading input parameters
> >>> Found PREFIX => snapshot
> >>> Found PATH => ./
> >>> Found COMPLEX => 1
> >>> Found RECEPTOR => 1
> >>> Found LIGAND => 1
> >>> Found COMPT => ./39981.prmtop
> >>> Found RECPT => ./1ijynow.prmtop
> >>> Found LIGPT => ./39981g.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
> >>> 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
> >>> Setting START to default 1
> >>> Setting STOP to default 10e10
> >>> Setting OFFSET to default 1
> >>> Setting VERBOSE to default 0
> >>> 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
> >> What's the problem here?
> >>
> >> HTH,
> >> Jason
> >>
> >> --
> >> Jason M. Swails
> >> Quantum Theory Project,
> >> University of Florida
> >> Ph.D. Candidate
> >> 352-392-4032
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun May 08 2011 - 09:30:03 PDT
