ch2lmp cannot find improper parameter, while included

Dear all,

I try to create a data file for PCLdiol (305 atoms). When running charmm2lammps.pl,
it appears a warning:

Warning: improper parameter 1 for [CG2O2 CG321 OG2D1 OG302 ] was not found
I have rechecked the pdb,psf, .rtf, .prm, but all the information about impropers are included. What can be the problem so that the improper parameter cannot be read, although it is included in parameter file.

I searched the mailing list, and found the same question was asked in 2012:
http://lammps.sandia.gov/threads/msg26309.html

However, there seems no following responses, and I am not sure if this question is solved.

Attached are my pdb, psf, rtf, prm

The prm and rtf file were extracted info from CHARMM General Force Field (CGenFF) for my ligand.

Thanks in advance,

AVOPCLdiol2000.pdb (23.9 KB)

AVOPCLdiol2000.psf (86 KB)

par_avopcldiol.prm (15.6 KB)

top_avopcldiol.inp (26.7 KB)

Dear all,

I try to create a data file for PCLdiol (305 atoms). When running
charmm2lammps.pl,
it appears a warning:
Warning: improper parameter 1 for [CG2O2 CG321 OG2D1 OG302 ]
was not found
I have rechecked the pdb,psf, .rtf, .prm, but all the information about
impropers are included. What can be the problem so that the improper
parameter cannot be read, although it is included in parameter file.

I searched the mailing list, and found the same question was asked in 2012:
http://lammps.sandia.gov/threads/msg26309.html
However, there seems no following responses, and I am not sure if this
question is solved.

​it isn't. ​you can see from the version history, that it hasn't been
changed since​ 2007

http://git.lammps.org/git/?p=lammps-ro.git;a=history;f=tools/ch2lmp/charmm2lammps.pl;hb=HEAD

Attached are my pdb, psf, rtf, prm
The prm and rtf file were extracted info from CHARMM General Force Field
(CGenFF) for my ligand.

​thanks for providing a *complete* set of inputs to reproduce the issue.​
the problem is easily identified when looking at the charmm2lammps.pl
script. it expects the heading of the section of improper parameters to be
named IMPROPER and not IMPROPERS. apparently, this is a change in CHARMM
that has been introduced long *after* charmm2lammps.pl was last updated.

the simple remedy is to edit your parameter file and rename IMPROPERS to
IMPROPER and it should work. i am now looking at finding a way to change
charmm2lammps.pl in a way, that it can accept both variants.

​axel.​

Thank you for the prompt reply, and the .data file now is successfully created without any warning.
Previously, I just make sure my .prm is with the same form as the one downloaded from CGenFF.

A related question is the number of atom types, the .data shows 0 atom_types.
However, when running ch2lmps, there is no warning, and in the created data file, it does find 8 types of atoms.
Is that a problem related to the inconsistency of CGenFF and Lammps?

Thanks again.

Best regards,
Yin

Thank you for the prompt reply, and the .data file now is successfully
created without any warning.
Previously, I just make sure my .prm is with the same form as the one
downloaded from CGenFF.

A related question is the number of atom types, the .data shows 0
atom_types.
However, when running ch2lmps, there is no warning, and in the created
data file, it does find 8 types of atoms.
Is that a problem related to the inconsistency of CGenFF and Lammps?

​there are no parameters for any atom types​ in your parameter file. where
should charmm2lammps.pl take them from?

axel.

Dear Axel,

Yes, I missed lines while revised the .prm so many times and so many versions. Thank you so much, the .data file is now created succesfully.