difficulties with ch2lammps for some pretty standard proteins including ubiquitin

Dear All,

ubq.pgn (212 Bytes)

1ubq.pdb (92.9 KB)

1ubq.psf (420 KB)

i cannot reproduce this with the current patch release (unstable) version of LAMMPS
using your files i get this:

$ perl charmm2lammps.pl all36_prot 1ubq -border=2.0 -cmap=36 -water -ions

charmm2lammps v1.9.1 ©2005-2016

Info: using 1ubq.pdb instead of 1ubq.crd
Info: lx not set: will use extremes
Info: ly not set: will use extremes
Info: lz not set: will use extremes
Info: creating PSF index
Info: creating fcc water
Info: changed lx to 34.4849 A
Info: changed ly to 34.4849 A
Info: changed lz to 39.4113 A
Info: converting atoms
Info: adding ions: [NaCl] = 0 mol/l (0 Na+, 0 Cl-)
Info: converting bonds
Info: converting angles
Info: converting dihedrals
Info: converting impropers
Info: conversion complete


Analyzing “1ubq.data”…

Total atoms: 4225
Total dihedrals: 3895
Total atom types: 37
Section “Masses” found: line 20
Section “Atoms” found: line 100
Section “Dihedrals” found: line 11361

Generating PHI/PSI dihedral pair list…

Carbon atom type/s: 11 12 13 14 15 16 17 18 19 20 21 22
Nitrogen atom type/s: 23 24 25 26 27 28 29
Peptide backbone carbon type: 11
Alpha-carbon type: 13
Alpha-carbon type (GLY): 14
Alpha-carbon type (PRO): 19
Peptide backbone nitrogen type: 26
Peptide backbone nitrogen type (PRO): 23
Terminal amino acid type is: GLY

Writing “1ubq.data” with section “CMAP crossterms” added at the end.