Regarding CHARMM22 FF with CMAP in lammps

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1

Dear ALL,

I would like to do protein-water simulation using CHARMM22 force field with CMAP in lammps. I was able to create the lammps data and input files by charmm2lammps.pl script using Charmm36 with CMAP (as given an example file). It was working without any issue. However, I am unable to create lammps data file using CHARMM22+CMAP (downloaded from http://mackerell.umaryland.edu/charmm_ff.shtml) I have tried for both the current and old versions of the FF i.e. taken from toppar_c36_jul18 and toppar_c32b1. I am obtaining following messages:

Using Charmm36
Info: converting bonds
Warning: bond parameter 2 for [SS SS ] was not found
Info: converting angles
Warning: angle parameter 2 for [SS SS SS ] was not found
Info: converting dihedrals
Warning: dihedral parameter 1 for [SS SS SS SS ] was not found
Info: converting impropers
Warning: improper parameter 1 for [SS SS SS SS ] was not found
Info: conversion complete

No carbon atoms exist in the system
No nitrogen atoms exist in the system
CMAP usage impossible

using charmm22
Info: converting bonds
Warning: bond parameter 1 for [ ] was not found
Warning: bond parameter 2 for [ SS ] was not found
.
Info: converting angles
Warning: angle parameter 1 for [ ] was not found
Warning: angle parameter 2 for [ SS ] was not found
.
Info: converting dihedrals
Warning: dihedral parameter 1 for [ SS ] was not found

.
No carbon atoms exist in the system
No nitrogen atoms exist in the system
CMAP usage impossible

The similar way I tested for charmm22 using toppar_c32b1. I am getting similar warning messages.

Could you help me regarding the above issue? Is there any way to create lammps data file using charmm22 FF with CMAP for the protein-water system.

Thank you very much for any help or suggestions you can provide.

With best regards,
Atanu

2

there is not enough information here to give any specific advice. please report all individual steps you did. and best also provide the (compressed) .psf/.pdb/force field) archive with an example that fails.

most importantly, the .psf file needs to be created with the same set of topology and parameter files as the conversion is done. otherwise atom types won’t match. you should also make certain, that you don’t have any strange characters like dos/windows carriage return characters in your files.

axel.