Ziyan Zhuang

4 Questions 6 Answers 0 Followers

Questions related from Ziyan Zhuang

How to use -merge program in GROMACS ?

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 3,096 1 View

What are your thoughts on the MD step at preprocessing?

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 8,379 4 View

How to solve this error in GROMACS?

" 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 2,439 0 View

How to settle the circumstance of molecular docking when charge=0 ?

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 1,542 1 View