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?
Thanks in advance
Sudipta
On Fri, Sep 13, 2013 at 11:51 PM, sudipta <sudipta.mml.gmail.com> wrote:
>
> 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
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
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>>
>>
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>
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Received on Sat Sep 14 2013 - 12:00:02 PDT
