Hello,
The stuff printed to stderr and stdout should contain your error messages.
What is actually printed out by MMPBSA.py to the screen? Or to wherever
stdout and stderr were redirected if that's the case.
All the best,
Jason
On Wed, Jun 30, 2010 at 9:10 AM, Bill Miller III <brmilleriii.gmail.com>wrote:
> Take a look at the _MMPBSA_*_gb.mdout and _MMPBSA_*_pb.mdout files. There
> should be some helpful information in those files.
>
> -Bill
>
> On Wed, Jun 30, 2010 at 6:47 AM, Asfa Ali <asfa.iisc.gmail.com> wrote:
>
> > Hi,
> >
> > I am running MMPBSA.py for the first time. The script I used for testing
> > is:
> >
> > Input file for running PB and GB
> > &general
> > startframe=5700, endframe=6000, interval=10, verbose=1,
> > # entropy=1,
> > /
> > &gb
> > igb=2, saltcon=0.100
> > /
> > &pb
> > istrng=0.100,
> > /
> >
> > I am getting all the _MMPBSA* files but in FINAL_RES_MMPBSA.dat, I get
> only
> > :
> >
> > | Run on Wed Jun 30 16:05:19 IST 2010
> >
> > |Input file:
> > |--------------------------------------------------------------
> > |Input file for running PB and GB
> > |&general
> > | startframe=5700, endframe=6000, interval=10, verbose=1,
> > |# entropy=1,
> > |/
> > |&gb
> > | igb=2, saltcon=0.100
> > |/
> > |&pb
> > | istrng=0.100,
> > |/
> > |
> > |--------------------------------------------------------------
> > |Solvated complex topology file: com143d_wat.prmtop
> > |Complex topology file: com143d_vac.prmtop
> > |Receptor topology file: 143d_rec_vac.prmtop
> > |Ligand topology file: lig_vac.prmtop
> > |Initial mdcrd(s): 143de2K_md2_agn.mdcrd
> > |
> > |Best guess for receptor mask: ":1-24"
> > |Best guess for ligand mask: ":25"
> > |Ligand residue name is "LIG"
> > |
> > |Calculations performed using 31 frames.
> > |Poisson Boltzmann calculations performed using internal PBSA solver in
> > sander.
> > |
> > |All units are reported in kcal/mole.
> >
> >
> -------------------------------------------------------------------------------
> >
> >
> -------------------------------------------------------------------------------
> >
> > No other information is given. Can u plz tell me where am I going wrong?
> >
> > Thanks a lot..
> > Asfa.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Jun 30 2010 - 07:30:14 PDT
