Hi all,
I have built a model of my system using psfgen and have got pdb files and psf files. I wish to use charmm2lammps to convert these to lammps. However when I use charmm2lammps I get this error message:
charmm2lammps v1.9.2 (c)2005-2018
Info: using Homo_sapien.pdb instead of Homo_sapien.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: converting atoms
Warning: 0 atom types present, but only 0 pair coeffs found
Info: converting bonds
Warning: bond parameter 1 for [ ] was not found
Info: converting angles
Warning: angle parameter 1 for [ ] was not found
Info: converting dihedrals
Warning: dihedral parameter 1 for [ ] was not found
Info: converting impropers
Warning: improper parameter 1 for [ ] was not found
Info: conversion complete
These are my input files:
Did you write a CHARMM or X-PLOR style (the default) PSF file in psfgen?
P.S.: you have not properly exported your google drive folder for sharing, so I cannot access your google drive files.
Yes I believe I did. Sorry about the google drive, hopefully this should work: charmm2lammps - Google Drive
When I look at your .psf file, I see that all atom types are set to -1.
The order of the columns in PSF files (according to the psfgen docs) are supposed to be:
atom ID, segment name, residue ID, residue name, atom name, atom type, charge, mass, and an unused 0. With the CHARMM format the atom type would be a number > 0, with the X-PLOR format a string.
39267 !NATOM
1 A 1 GLN N -1 -0.300000 14.0070 0
2 A 1 GLN HT1 -1 0.330000 1.0080 0
3 A 1 GLN HT2 -1 0.330000 1.0080 0
4 A 1 GLN HT3 -1 0.330000 1.0080 0
5 A 1 GLN CA -1 0.210000 12.0110 0
6 A 1 GLN HA -1 0.100000 1.0080 0
7 A 1 GLN CB -1 -0.180000 12.0110 0
Without the chance to identify atom types, charmm2lammps.pl cannot function, since the atom types are crucial for identifying the force field parameters, bonded and non-bonded. If I look at the two examples in tools/ch2lmp/example/ and tools/ch2lmp/example-cmap/ they seem to be using either convention. But in both cases, the atom types can be identified, unlike in yours.