Charmm2lammps tool

LAMMPS LAMMPS General Discussion
1

Dear LAMMPS users,
I am trying to mix heptadecane with graphene in CHARMM FF and conversed subsequently to the LAMMPS data file using charmm2lammps v1.9.2. Graphenes are located randomly in heptadecane.

Firstly, I pack the heptadecane and graphene using packmol. Subsequently, I try to generate psf file (Mixed-Hepta-Graphene.psf) and pdb (Mixed-Hepta-Graphene.pdb) file in VMD using top_all36_cgneff.rtf and top_all36_lipid.rtf for graphene and heptadecane, respectively. I try to generate the LAMMPS data file separately using charmm2lammps and obtain two LAMMPS data files (LAMMPS-all36_cgenff.data & LAMMPS-all36_lipid.data).
But, the results show as follows:

Generating LAMMPS data using all36_cgenff:
perl charmm2lammps.pl all36_cgenff Mixed-Hepta-Graphene

Info: using MixedHeptaGraphene1.pdb instead of MixedHeptaGraphene1.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 [ ] 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
Info: conversion complete

Generating LAMMPS data using all36_lipid:
perl charmm2lammps.pl all36_lipid Mixed-Hepta-Graphene

Info: using MixedHeptaGraphene2.pdb instead of MixedHeptaGraphene2.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: 5 atom types present, but only 4 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
Info: conversion complete

I am also wondering how to generate LAMMPS data using two different Topology files (top_all36_cgneff.rtf & top_all36_lipid.rtf) for the mixture. Is it possible to generate single LAMMPS data using two different topology files?

All attached files are saved in the following link: LAMMPS - Google Drive

I will be so grateful for any helpful comments and suggestions.

Regards,
Togi

2

The problem is not the topology file but the force field parameter file.
As you can see from the Masses section, some atom types are not recognized in either of the two data files. You need to use a (combined) parameter file that has entries for all atom types (and bond/angle/dihedral/improper types).

As I have mentioned before, your original .psf file is flawed. If I visualize it in VMD you can see lots of incorrectly assigned bonds. So even after fixing the issue with the force field parameter assignment, you still will have to revise your procedure of building the topology.

vmdsnapshot
vmdsnapshot1074×985 290 KB

3

Dear Axel,
Thank you very much for your response.

The step to generate *.psf file is initially conducted by extracting the heptadecane (30xHeptagraphene-HeptaPymol.pdb) and graphene (30xHeptagraphene-GraphenePymol.pdb) from the packed one (30xHeptagraphene.pdb) using PyMol. In details, I used the following commands to generate *.psf (MixedHeptaGraphene.psf) file:

package require psfgen
resetpsf
topology top_all36_lipid.rtf
topology top_all36_cgenff.rtf
pdbalias residue ALK HEP
pdbalias residue GP0 GRA
segment A {pdb 30xHeptagraphene-HeptaPyMol.pdb}
segment B {pdb 30xHeptagraphene-GraphenePyMol.pdb}
coordpdb 30xHeptagraphene-HeptaPyMol.pdb A
coordpdb 30xHeptagraphene-GraphenePyMol.pdb B
regenerate angles dihedrals
guesscoord
writepdb MixedHeptaGraphene.pdb
writepsf charmm MixedHeptaGraphene.psf
exit

All files are shared in the link I sent before.
Any comments and suggestions are greatly appreciated.

Regards,
Togi

4

Sorry, but this is not a LAMMPS issue but rather a NAMD/CHARMM/psfgen issue. Something you are doing is obviously not correct. Could be the commands, could be the files. You need to debug this using the corresponding documentation and - if needed - ask in the corresponding forums. I suggest you start with a single small molecule and debug that and gradually build your skills. It is quite worrying, that you keep doing things without checking and only ask for help when operations fail. You have to take into account that things can go wrong without explicit errors.

5

Dear Axel,
Thank you for your suggestions.
I am sorry for the inconvenience.

Regards,
Togi