Hi Jason,
Thank you very much for your reply. Again, there is a problem, the chamber
program uses only charm formatted psf file. However, I generated .psf using
psfgen package and that .psf file is not compatible with chamber. Is there
any way to convert NAMD generated .psf to CHARMM generated psf.
These are following output that I got after running CHAMBER
| *****************************************************
| * CHAMBER: Charmm psf to AMBER prmtop convertor *
| * *
| * v1.0 *
| * *
| * Written by: *
| * Mark J. Williamson *
| * Michael F. Crowley *
| * Ross C. Walker *
| * *
| *****************************************************
At line 2785 of file psfprm.F90 (unit = 20, file =
'3zzb_protein_ligand_system_gc1.psf')
Fortran runtime error: Bad value during integer read
And my command line was
/home/sudipta/Downloads/amber12/bin/chamber -top
/home/sudipta/NUC_RECEPTOR/MISC/ff/toppar/top_all27_prot_na.rtf -top
/home/sudipta/WORK/FEP/SYSTEM_3JZC/top_thyroid.inp -param
par_all27_prot_na.prm -param par_thyroid.inp -psf
3zzb_protein_ligand_system_gc1.psf -crd 3zzb_protein_ligand_system_gc1.pdb
-p 3jzb_test.prmtop -inpcrd 3jzb_test.inpcrd -cmap
On Fri, Sep 13, 2013 at 11:53 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Fri, Sep 13, 2013 at 11:28 AM, sudipta <sudipta.mml.gmail.com> wrote:
>
> > Hi Daniel,
> >
> > Yes, you are right. I can able to convert DCD file to amber .mdcrd file.
> >
>
> As Dan said, you do _not_ need to convert DCD files to amber .mdcrd since
> MMPBSA.py uses cpptraj for trajectory processing, so any trajectory
> recognized by cpptraj is recognized by MMPBSA.py (this includes DCD).
>
>
> > But I can't convert the .prmtop file from .psf and charm parameter files.
> > As far as I know there is some limitation on MMPBSA program which uses
> only
> > amber .prmtop file. If you have any idea how to do that please let me
> know.
> >
> >
>
> Yes, MMPBSA.py calls amber programs to compute energies, so you must use
> Amber topology files. If you are using the CHARMM force field, then you
> need to use chamber (see chapter 2, section 11 of the AmberTools 13 manual
> near page 45 or so).
>
> As a note, you will need to have Amber12 installed (with sander) in order
> to use MMPBSA.py on a chamber-generated topology. The reason is that
> CHARMM energy terms are only supported in sander and pmemd (not NAB, which
> is the program in AmberTools that MMPBSA.py would otherwise use to compute
> energies).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
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Received on Fri Sep 13 2013 - 10:30:02 PDT
