GROMACS version: 2023.3
GROMACS modification: No
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Hello everyone, I am a newbie that still learning MD and trying to perform MD simulation on 2AZ5 protein which is TNF-alpha that posses 4 chains [A,B,C,D] and a small inhibitor molecule.
I have cleaned the protein and maintained chain A and B as the dimer is important in the binding and fixed the missing residues using MOE.
When i run pdb2gmx command to get .gro file it gives me an error that there is missing ASP that is not found in the library so I want to inquire how to correctly fix missing residues/atoms before performing MD simulation.