GROMACS version:2023
GROMACS modification: Yes/No
I am writing to seek assistance on a matter related to n2t file generation. I am using charmm36 force field in my work. I am covalently attaching a short polymer to a nanosheet with the carbonyl carbon of the polymer attached to the nitrogen of the nanosheet I obtained the parameter(itp file) for the poly-peptide from CGENFF then added the corresponding atom types and charges from the itp to my n2t file the monomer of the poly-peptide is histidine and it’s itp file has various hydrogen atom type along with carbon types with different charges I have added them all in the n2t file in the same sequence as in the itp since most these atom types are attached to carbon when topology is created using x2top wrong type of carbon and consequently wrong charge is assigned to the atom of my structure. I want you to note the hydrogen types as well as the nitrogen type NG2R51 in the topology file at line 134 it is supposed to be a NG2S1 nitrogen type with a -0.555 charge. There are many other atoms whose atom type was supposed to be different. Since I am a beginner and don’t have much knowledge on on how to solve this issue, I cannot manually correct the topology as I want to add 4 chains in total with almost 8 monomers each in the final system. Any guidance or pointers would be of immense help. Thank you for your time.
n2t file
itp file
topology
