GROMACS modification: No
I am trying to include Hydronium ions (H3O)+ in to my system and I have a stream file (.str) and input file (.inp) developed from a research group.I know using the python script in http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs can obtain .itp .prm files from CGenFF generated stream file.
But is there any method that I can get .itp and .prm files from non-generated .str file?
For a molecule with 4 atoms, 3 bonds, and 3 angles, I would just write the topology by hand. It will probably be faster than trying to write a converter.
Thank you for the feedback. I am new to MD simulations so I tried to find a protocol that can lead me to understand how to build the topology,but I couldnt find. Do you know where I can find ?
Also, I found ffTK in VMD can generate CHARMM parameter file ,so I would like to know can I use cgenff_charmm2gmx_py3_nx2.py` script to convert my parameters obtained with FFTK into GROMACS format?
I found here ,someone has done it,Atom types equivalence between CHARMM36 and AMBER99bsc1
Note from my reply that it is not possible to transform one force field into another, but such a topic is not relevant to what you’re doing.
Start with a known system that works. Study it and make sure you understand it, and refer to the GROMACS manual to understand the requisite file formats. One such example that may be useful: Protein-Ligand Complex