GROMACS version: gmx22
GROMACS modification: No
Hi, I am new at using gromacs and I have a molecules, which consists of 2 amino acids, and a chlorophyll a molecule. The amino acids get recognized, but I need an rtp file for the Chlorophyll. I have just my self-built .pdb-file and have seen an .rtp.example in the gromacs manual. In this example are charges included, where I don’t know, how to get them. Also, can someone please show me also, how to build a tailored .rtp-file for my molecule?
I would suggest generating a separate .itp file, instead of an .rtp file, for molecules that are not proteins, DNA, RNA and (possibly) lipids.
There are many ways to generate parameters for other molecules, e.g., CGenFF, ACPYPE or STaGE. But I think you will have a hard time generating good parameters for such a complex molecule as chlorophyll.
Thank you - how do I generate an itp-file? Is there a command for this in gromacs?
As I wrote in my previous reply, there are a number of different tools available, some specifically for one force field, e.g CGenFF, and some more general, e.g. STaGE. You should make sure that you are generating parameters that are compatible with the rest of the force field you are using.
You might get some useful information from Protein-Ligand Complex.