charmm2lammps

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1

Prelims: we tried charmm2lammps to convert an existing NAMD project to
lammps, and it succeeded without warnings.

We now try a slightly larger project, and see:

$ perl charmm2lammps.pl nachr nachr-uS5chol2ach

charmm2lammps v1.9.1 (c)2005-2016

Info: using nachr-uS5chol2ach.pdb instead of nachr-uS5chol2ach.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
Info: converting bonds
Warning: bond parameter 1 for [ CRL1] was not found
Warning: bond parameter 2 for [ CRL2] was not found
Info: converting angles
Warning: angle parameter 1 for [ CRL1 CRL1] was not found
Warning: angle parameter 2 for [ CRL1 CRL2] was not found
...

It looks as though there is a blank as one of the "atoms" in each
warning. I'm guessing that as NAMD is happy with those input files,
it is somehow more lenient than charmm2lammps? I am having a hard
time figuring out what is missing, as the warning happens after
"everything" is parsed, and noting which lines have empty parameters.

Any clues on how to debug this?

Best wishes,

Patrick

2

Prelims: we tried charmm2lammps to convert an existing NAMD project to
lammps, and it succeeded without warnings.

We now try a slightly larger project, and see:

$ perl charmm2lammps.pl nachr nachr-uS5chol2ach

charmm2lammps v1.9.1 (c)2005-2016

Info: using nachr-uS5chol2ach.pdb instead of nachr-uS5chol2ach.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
Info: converting bonds
Warning: bond parameter 1 for [ CRL1] was not found
Warning: bond parameter 2 for [ CRL2] was not found
Info: converting angles
Warning: angle parameter 1 for [ CRL1 CRL1] was not found
Warning: angle parameter 2 for [ CRL1 CRL2] was not found
...

It looks as though there is a blank as one of the "atoms" in each
warning. I'm guessing that as NAMD is happy with those input files,
it is somehow more lenient than charmm2lammps? I am having a hard

it would be more correct to state, that charmm2lammps is more stuck in
the past than NAMD. the core of its code is assuming that you are
using CHARMM from over 10 years ago. unfortunately, the code in
charmm2lammps is not very easy to read and understand due to its
"creative" use of perl constructs, thus it hasn't been updated much
since its original inception.

time figuring out what is missing, as the warning happens after
"everything" is parsed, and noting which lines have empty parameters.

Any clues on how to debug this?

the first thing to make certain of, is that your psf file is in CHARMM
format and not in X-PLOR style (as preferred by NAMD).

the second thing to look at would be which type of atom is connected
to CRL1 and CRL2 and check if any of those have "unusual" atom types
which the heuristics in charmm2lammps may not consider valid.

next, you can compare the input PSF with the control PSF file to
check, if there are any significant discrepancies.

hopefully, one of these will resolve your problems.

axel.