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Questions related from Ziyan Zhuang
Command line: gmx_mpi -merge -f XXX.gro heme.gro -o complex.gro Error in user input: Invalid command-line options In command-line option -merge Invalid value: heme.gro In command-line...
14 April 2024 3,094 1 View
I merged heme and a ligand by manually editing gro and top instead of “-merge”, after which MD was performed. This result was unexpected for me because heme is not covalent binding to the protein,...
14 April 2024 8,377 4 View
" Back Off! I just backed up topol_Other_chain_A2.itp to ./#topol_Other_chain_A2.itp.2# Making bonds... atom HA is missing in residue HEM 600 in the pdb file atom HA is missing in residue HEM...
13 April 2024 2,438 0 View
And I was using imidacloprid for molecular docking. When setting the ligand, the charge of imidacloprid was always calculated to be 0, and the docking reality was wrong.
25 November 2023 1,539 1 View