Hi Jason,
I can create the prmtop file without any error using chamber. I have made
all the prmtop file using chamber and converted my namd .dcd file to .mdcrd
rajectory file. However, there is some problem to run it. The errors are
following below.
time MMPBSA.py -O -i mmpbsa_ptraj.in -o FINAL_RESULTS_MMPBSA_NMODE.dat -sp
3jzb_test.prmtop -cp 3jzb_complex.prmtop -y
3jzb_protein_ligand_system_12.mdcrd
Loading and checking parameter files for compatibility...
ValueError: invalid literal for int() with base 10: '8('
Exiting. All files have been retained.
On Sat, Sep 14, 2013 at 7:18 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Sat, Sep 14, 2013 at 2:55 PM, sudipta <sudipta.mml.gmail.com> wrote:
>
> > Hi Ross,
> >
> > I have generated charm formatted psf file using charmm progarm. The
> chamber
> > program successfully reads that .psf file. Moreover, it also finds the
> > right atom types and nonbonded parameters. After that, I am getting some
> > strange errors. I don't understand the details of that errors. Please
> help
> > me out in this regard. The output looks like
> >
> > | *****************************************************
> > | * CHAMBER: Charmm psf to AMBER prmtop convertor *
> > | * *
> > | * v1.0 *
> > | * *
> > | * Written by: *
> > | * Mark J. Williamson *
> > | * Michael F. Crowley *
> > | * Ross C. Walker *
> > | * *
> > | *****************************************************
> >
> > EXTented file format is being used
> >
> > ===========================================================
> > PSF input parsing summary
> > ===========================================================
> >
> > Number of PSF flags found: 4
> >
> > Number of atoms found: 70725
> > Number of residues found: 22432
> >
> > Number of bonds found: 70758
> > Number of angles found: 29949
> > Number of dihedrals found: 11405
> > Number of impropers found: 693
> >
> > Number of donors found: 443
> > Number of acceptors found: 22558
> > Number of explicit nonbonded exclusions found: 0
> >
> > Number of groups found: 23413
> > Number of ST2 waters found: 0
> >
> > Number of cross terms found: 261
> > ===========================================================
> >
> > --- Found all ATOM TYPES in topology file
> >
> > --- Found all nonbond parameters
> > At line 641 of file psfprm.F90
> > Fortran runtime error: Bad value during floating point read
> >
> > By the way my system contains protein and ligand and they have their own
> > separate parameter and topology files. I just combined them by cat
> command
> > and make a single file. Is there any wrong with it?
> >
>
> I do not think you can simply concatenate two PSF files (you certainly
> cannot do that with two PRMTOP files).
>
> I believe you need one PSF file for the combined system. Also,
> ante-MMPBSA.py will not work with chamber topology files, so you will need
> to make sure that you make each one that you need using chamber.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Sat Sep 14 2013 - 19:30:02 PDT
