GROMACS version: Any, but I am using 2020.1
GROMACS modification: No
Hi guys, hopefully you will be able to help me out with this. I am trying to use gromacs to simulate a DNA nanostructure, in which some of the 3’ terminal residues are modified with a cholesterol, attached via a tetra ethylene glycol linker (TEG-Cl), using the charmm36 ffs.
I can generate the charmm36 parameters for the TEG-Cl using cgenff, or swissparam, and these have been pretty sufficient for some previous, similar work I have done, which was performed in NAMD.
I have been able to generate NAMD style .psf topologies using psfgen by ammending the swissparam generated .rtf to my nucleic acids topology and applying it as a 3’ terminal patch. However I would really like to be able to achieve this in gromacs (The dream would be to build the system in charmn-gui).
So I have generated the parameters and topologies for my TEG-Cl, oriented it correctly in VMD and concatenated the pbd files. I have no problems using the swissparam topologies to treat the TEG-Cl as a ligand, but am struggling to register it as part of the DNA chain.
It is my understanding that I will need to edit the merged.rtp in my charmm ff folder to add an entry for the TEG-Cl, using the swissparam outputted .itp as a base. I am running into a little trouble here as the swissparam .itp has a few more columns than my merged.rtp.
Will I also need to modify ffbonded.itp if I want to have the TEG-Cl bonded the rest of the DNA? and are there any other parts of the forcefields I would need to adapt?
let me know if there is any more info that would be useful, I can ofc provide the coordinate & parameter files if you think that would be useful.
All the best,