GROMACS version: 2022.5-Debian_2022.5_2
GROMACS modification: No
Hello all,
I have a double bilayer system with one integral membrane protein in each bilayer that’s been running for over 12 µs. The system was originally set up by building a monolayer in CHARMM-GUI, then “stacking” a copy of that system using a series of GROMACS commands.
I’m now trying to modify several residues in one of the protein monomers. My first approach was to edit the protein in the CHARMM-GUI PDB Reader, replace the original protein with the modified one, and generate a new PDB file with the updated residues.
The issue I’ve run into has to do with how CHARMM-GUI handles the NH₃⁺ and COO⁻ termini. The N-terminal Asp residue doesn’t match the CHARMM36m parameters, which causes pdb2gmx to throw the following error:
Atom HT3 in residue ASP 20 was not found in rtp entry ASP with 14 atoms
while sorting atoms.
Using the -ignh option doesn’t work because of the TIP3P waters. If I run pdb2gmx on the protein alone—without the membrane, waters, or ions—it completes just fine.
Is there another way to modify the protein structure for use with GROMACS? Or would it be possible to piece together the topology to continue the simulation?
Any advice would be greatly appreciated.
Thanks for your time,
Kyle