Improper parameter missing, though included.

Dear all,

I¡¯m developing a Charmm force field file of a small molecule.

Firstly, I¡¯ve used Charmm-gui input generator to create topology and parameter file from pdb file, and then PSF generator from VMD to generate psf file.

All these processes go without any problem. But when I try to convert the psf file into lammps data and input file with, a warning message occurs saying that improper parameter of [CG2R53 NG2R53 NG2R53 OG2D1] is missing. As you can confirm from the attached prm file, the improper parameter of [CG2R53 NG2R53 NG2R53 OG2D1] is clearly included.

Although this is just a warning, when I actually try to start an MD simulation, the simulation fails because of the error from the missing parameter.

I have tried all I can think of, but failed to solve the problem.

What can be the problem so that the improper parameter cannot be read, although it is already included?

The attached files are:

the pdb file including the coordinates of my ligand of interest.

The prm and rtf file were originally from Charmm general force field, and extra info for my ligand is added. In rtf file, BOND and IMPR info is added under the ligand name CB6, and in prm file, some required parameters are added at the end of BONDS, ANGLES, DIHEDRALS, IMPROPERS.

The autopsf files(pdb, psf) are generated by using VMD PSF generator with prm and rtf file.

Many thanks in advance,


P.S. I thought maybe this is related. The generated data file by using charmm2lammps(though warning does occur), the number of atom types are different.

There are eight atom types, but only six are listed. This itself cause a problem when running LAMMPS simulation. I¡¯ve put missing parameters manually and the errors disappear, but then the improper parameter problem comes up.

cb6_heta.pdb (8.34 KB)

cb6_heta_autopsf.pdb (8.49 KB)

cb6_heta_autopsf.psf (31.2 KB)

par_all36_cgenff.prm (472 KB)

top_all36_cgenff.rtf (1.22 MB)

Maybe Paul can look at this ... he helped create the chm2lmp tool.


Pieter in't Veld is the expert on the details of the script. I've asked him to take a look --- we'll see what he says.