GROMACS version: 2023.2
GROMACS modification: Yes/No
Hello everyone,
I have a question about creating a pdb file to be used in MD simulation. I use GROMACS 2023.2 on Google Colab. I work with the protein 1dn2, and I removed the engineered residues from the structure. The protein is dimerized in antiparallel configuration. When I want to use CHARMM GUI input generator to create the proper box for MD simulations, I get an unusually long and unnecessary bond between two chains. The generator automatically joins two chains from the first chain’s C-terminus with the second chain’s N-terminus, which are in the opposite direction and they are placed far from each other. The dimer interacts through the chains’ C-termini. How can I solve this problem?