Dear Gromacs Users, I would like to perform MD simulations of protein with ligand molecule. Now I am preparing ligand parameter using CGenFF similar with Gromacs Tutorial #5. However, CgenFF gives an error as following: Hypervalent carbon (valence=5) not supported CGenFF. If you have any experience, please let me suggest other possibility to prepare parameter of ligand molecules…

GROMACS version: VERSION 5.1.1 GROMACS modification: Yes/No Here post your question Dear experts, While using ions.tpr command line I am facing errors. Forcefield used: charmm36-mar2019.ff Command line: gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr Ignoring obsolete mdp entry ‘title’ Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# NOTE 1 [file ions.md…

GROMACS version: 2022.3 GROMACS modification: Yes/No Hi there, I am struggling to run gmx do_dssp. I have tried several options. Here it is: gmx do_dssp -s sim_eq-3.tpr -f sim_eq-3.xtc -o -sc -ver 4 after selecting MainChain I got: There are 299 residues in your selected group dssp cmd=‘/group/davila/SOFTW/COMPCHEM/bin/dssp --output-format dssp ddhzTGP0’ Reading frame …