It works!
Thanks very much Jason.
On Mon, Feb 1, 2016 at 6:08 PM, Jason Swails <jason.swails.gmail.com> wrote:
> I would suggest trying to use ParmEd instead of chamber to convert CHARMM
> files to Amber. In addition to improved support for a wider variety of PSF
> file formats, it also supports NBFIX modifications (which chamber does
> not).
>
> There are instructions for using it in the Amber manual.
>
> HTH,
> Jason
>
> On Mon, Feb 1, 2016 at 4:09 PM, Gary Zhang <yz146.duke.edu> wrote:
>
> > Dear Amber Community,
> >
> > I am using chamber to convert a set of charmm topology and parameter
> files
> > of protein and ligand to amber format. I am having troubles with some
> > molecules when having a non-aromatic ring. The command I am using is:
> >
> > chamber -cmap -str SFG.str -top all.rtf -param all.prm -xpsf first.psf
> -crd
> > first.pdb -p AMBER-System.prmtop -inpcrd AMBER-System.inpcrd
> >
> > all.rtf and all.prm are two files with all topology and ff parameters
> from
> > original charmm36. first.psf and first.pdb are two files that generated
> by
> > vmd script. SFG.str is a charmm file of the ligand generated by
> paramchem.
> >
> > The output message from chamber is:
> >
> >
> > | *****************************************************
> > | * CHAMBER: Charmm psf to AMBER prmtop convertor *
> > | * *
> > | * v1.5 *
> > | * *
> > | * Written by: *
> > | * Mark J. Williamson *
> > | * Michael F. Crowley *
> > | * Ross C. Walker *
> > | * Jason Deckman *
> > | * Robin M. Betz *
> > | * *
> > | *****************************************************
> >
> > EXTended file format is being used
> >
> > ===========================================================
> > PSF input parsing summary
> > ===========================================================
> >
> > Number of PSF flags found: 3
> >
> > Number of atoms found: 53030
> > Number of residues found: 16226
> >
> > Number of bonds found: 37221
> > Number of angles found: 25876
> > Number of dihedrals found: 14756
> > Number of impropers found: 949
> >
> > Number of donors found: 0
> > Number of acceptors found: 0
> > Number of explicit nonbonded exclusions found: 0
> >
> > Number of groups found: 1
> >
> > Number of cross terms found: 342
> > ===========================================================
> >
> > --- Found all atom types in topology file
> >
> > WARNING: No NONBONDED parameter section in this stream file:
> > | /home/yz146/mmpbsaNAMD/sfg/SFG.str
> >
> > --- Found all nonbond parameters
> > Segmentation fault
> >
> >
> > While everything went through for other molecules without non-aromatic
> > rings.
> > Has anyone met with this issue before?
> >
> > Any hint or clue will be greatly appreciated.
> >
> > Thanks very much.
> >
> > Best.
> > Gary Zhang
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> 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 Tue Feb 02 2016 - 07:00:04 PST
