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
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Feb 01 2016 - 15:30:03 PST
