GROMACS version: 2023
GROMACS modification: Yes/No
I am getting one very unphysical coordinates for one of the hydrogens added into the ARG amino acid of my protein (shown in image below) from the .gro file outputted after pdb2gmx. This is preventing me from running the later steps of the MD simulation process. Any way to fix this error?
How did you add the hydrogen atom? pdb2gmx add hydrogen atom as per the ff. Looks like you edited the pdb and lost its structure/style
I did not manually add in the hydrogen atom. I removed unnecessary heterogeneous atoms from the PDB file, but those are not hydrogen atoms. This hydrogen atom with unphysical coordinates was added in by pdb2gmx using the Amber-99 Force Field. But why would it add such a coordinate for the hydrogen atom?
