Hello, after running MD production for my antigen and Fv complex using GROMACS 2025.4, I applied the following preprocessing commands and exported a specific frame conformation (colored green). When viewing the original conformation (cyan) alongside the exported conformation (green) in PyMOL, long straight lines (marked in red) are observed in the green structure. These lines are discontinuous, and their general trend extends from one chain terminus of the antigen to a chain terminus of the antibody. These lines are absent in the original conformation and cannot be removed. 1. What is the cause of these line segments? 2. Is there any way to remove them? 3. If they cannot be removed, will this affect my subsequent analysis? The preprocessing and export commands are as follows:
- gmx convert-tpr -s md5.tpr -o md5_protein.tpr
- gmx make_ndx -f md5_protein.tpr -o index_md5_protein.ndx
- gmx trjconv -s md5.tpr -f md5.xtc -o md5_cluster.xtc -pbc cluster -center
- gmx trjconv -s md5.tpr -f md5_cluster.xtc -o md5_mol.xtc -pbc mol
- gmx trjconv -s md5.tpr -f md5_mol.xtc -o md5_fit.xtc -fit rot+trans
gmx trjconv -s md5_protein.tpr -f md5_fit.xtc -dump 147950 -o cluster1_025nm_147950ps.pdb