GROMACS version:2021.4
GROMACS modification: Yes/No
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Hello Gmx community.
I am trying to create a topology file for an RNA system containing pseudouridine (and possibly afterwards, other post transcriptional modifications). I successfully built the topology file for the PSU residue and included it in the rtp file of the force field I am using. I also modified accordingly the residue types.dat. My issue concerns the rna.hdb file for adding hydrogens to my system using pdb2gmx. I know I should add 11 hydrogens atoms that gmx finds missing when trying to build the topology file, but I cannot figure out how to properly modify the rna.hdb file for my PSU nucleotide.
I would be grateful for any help or explanation concerning the different columns in, and therefore how to modify this file :)
Thanks a lot.
Laura TROUSSICOT, PhD.