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 - 16:30:02 PDT
