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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Fri Sep 13 2013 - 11:00:03 PDT
