Thank you for the reply. But I am unable to find where the error is. The
solvated prmtop is consistent with the trajectory i have given in -y flag.
But for the mdcrds the MMPBSA.py created the structures were distorted. The
masks are matching in the namelist. Please let me know how can I spot the
error I tried to attach the prmtop files but failed.
On Tue, Apr 20, 2010 at 5:06 PM, Bill Miller III <brmilleriii.gmail.com>wrote:
> What file(s) did you get these errors from? Do the mdout files have any
> errors in them? The ************* for VDWAALS energy is usually indicative
> of an inconsistency in the prmtop files. You should check to make sure that
> all the prmtop files you provided match with the masks that you set in the
> &general namelist. A good way to check this is to use the prmtops to
> visualize the mdcrd complex, receptor, and ligand mdcrds that MMPBSA.py
> creates. Also make sure the solvated prmtop you provided is consistent with
> the trajectory that you provided in the command line after the '-y' flag.
>
> I hope that helps.
>
> -Bill
>
> On Tue, Apr 20, 2010 at 6:31 AM, Hyma vathi <hymavathi.niper.gmail.com
> >wrote:
>
> > Hi all,
> > I am trying to perform MMPBSA to calculate the binding free energy of a
> > protein-ligand complex. The following error message has resulted, can
> > anyone
> > please what might be the reason. Thank you in advance.
> >
> > This is my input file : mmpbsa.in
> >
> > Input file for running PB and GB in serial
> > &general
> > startframe=1,endframe=200,interval=1, keep_files=2,
> > receptor_mask=':1-316', ligand_mask=':317',
> > /
> > &gb
> > igb=2, saltcon=0.100,
> > /
> > &pb
> > istrng=0.100,
> > /
> >
> >
> > Bad data for namelist object igb
> > namelist read: missplaced = sign
> > Bad data for namelist object igb
> > Bad data for namelist object igb
> > namelist read: missplaced = sign
> > Error: Sander output is missing values!
> > VDWAALS = ************* EEL = -10641.5711 EGB =
> > -6880.1883
> >
> >
> >
> > --
> > Hymavathi,
> > MS(Pharm),
> > Center for Pharmacoinformatics,
> > National Institute of Pharmaceutical Education and Research(NIPER),
> > Mohali,
> > INDIA.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
Hymavathi,
MS(Pharm),
Center for Pharmacoinformatics,
National Institute of Pharmaceutical Education and Research(NIPER),
Mohali,
INDIA.
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Received on Tue Apr 20 2010 - 08:30:03 PDT
