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.
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Received on Tue Apr 20 2010 - 05:00:03 PDT
