GROMACS version: 2024.5
GROMACS modification: No
Hello to everybody!
I’m using CGenFF to parametrize my ligand and start the MD run with GROMACS2024.5 (charmm36ff - tip3p water model). I have an issue only with molecules containing halogens like Cl and Br. I think the main problem might be with the lone pairs (LP/LPH). When I keep them inside .gro or .itp files and so on, I get:
Command line:
gmx mdrun -v -deffnm em
Reading file em.tpr, VERSION 2024.5 (single precision)
Update groups can not be used for this system because an incompatible virtual site type is used
Segmentation fault (core dumped).
When I remove the LP from all the files, I can perform the minimization, but the em.gro file that I visualize is wrong: the Br (for example) is not bonded, and the molecule is no longer planar but is folded in on itself, like it’s crumpled.
Can somebody help me fixing this?
Thank you