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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Received on Mon Feb 01 2016 - 13:30:03 PST
