Hi Ross,
I had freshly installed the AMBERTOOLS13 with all updates. But still, I am
getting the same error.
At line 2793 of file psfprm.F90 (unit = 20, file =
'3zzb_protein_ligand_system_gc1.psf')
Fortran runtime error: Bad value during integer read
Are the x-plor psf and psfgen psf format same
On Fri, Sep 13, 2013 at 1:31 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Sudipta,
>
> Use Chamber from AmberTools 13 with all the latest updates. It supports
> XPLOR psf's.
>
> All the best
> Ross
>
>
> On 9/13/13 10:20 AM, "sudipta" <sudipta.mml.gmail.com> wrote:
>
> >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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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
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>
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Received on Fri Sep 13 2013 - 21:00:02 PDT
