I’m interested in using EMC to construct some initial configurations for a CHARMM-based system. I’ve been exploring using CHARMM-GUI to construct some parts of my system, such as polyethylene or silica nanoparticles defined with parameters of the Interface Force Field, but want to try to use EMC with CHARMM. In the emc/field/charmm/ directory, there are several pairs of EMC-style .top and .prm files, all of which say they were converted using emc_charmm.pl. I couldn’t find this file in the emc/scripts/ directory - is it stored somewhere else, or perhaps not included in EMC?
The emc_charmm.pl script is currently not part of the EMC distribution. However, all provided charmm/c36a force fields have been converted from the original data as provided by the MacKerell group. This conversion is based on all residues as present in the original topology files. EMC provides typing beyond the original residues due to the fact that its typing rules are based on chemical environment. This in contrast to the classical templated-based approach of the original CHARMM force fields.
As an aside, EMC can import .pdb and .psf. EMC needs the .psf for connectivity. A normal approach for using EMC in combination with .pdb from the Protein Databank is to prepare a .pdb and .psf pair with VMD. Here one can also add missing hydrogens etc. Using EMC to create input for protein simulations allows for building complex mixtures around the protein structure at condensed matter conditions. The upcoming EMC release will include ports to NAMD and GROMACS next to the already existing port to LAMMPS. Both NAMD and GROMACS ports are also integrated into the EMC workflow agent. Analysis routines will not be as rich as for LAMMPS due to the limited on-the-fly analytic routines in NAMD and GROMACS. The next release is expected to be ready for July 1 of this year.
Thank you for your reply! I will take a closer look at the charmm/c36a files and see what I can do. The biggest thing that I would want to change is to add a few simple atom types which are present in the CHARMM-style description of SiO2 in Chem. Mater. 2014, 26, 8, 2647–2658 (https://doi.org/10.1021/cm500365c). I have a .prm file for these parameters, so perhaps since it’s only a few atom types/bonds/angles I could add them manually to an existing set of EMC force field files.
Ah, I understand. The new release of EMC will allow you to add new parameters and rules to an existing force field through ITEM FIELD. This will combine existing .prm and .top files into one new .prm, the latter of which will also contain the newly added parameters. This might help you along the way for your added SiO2 parameters.
I see that you are referring to an IFF paper of Hendrik Heinz and coworkers. We are in the works of adding IFF contributions to EMC as separate force fields, which in turn can be used to apply to parts of the simulation.