[gmx-users] Procedure for processing docked complex from Autodock vina

Dear all, I am trying to run a simulation of protein docked with ligands of interest. I have used autodock vina for the docking. Do i need to convert the receptor.pdbqt to receptor.pdb before proceeding? Do i need to add missing hydrogens in this step? Also the protein of interest has four

Re: [gmx-users] Response required

Your using more atoms than LigParGen allows. Try generating a topology for a trimer, tetramer, and pentamer (if you can) and then use the resulting output topologies as a template for building 3 types of PEO residues: 1 with a linkage to the beginning of the chain, 1 with a linkage to the end

Re: [gmx-users] Help w.r.t enhancing the node performance for simulation

Dear all, I was able to overcome the issue, by introducing the command "mpirun -np x" before the command. Here is the exact command- mpirun -np 32 gmx_mpi mdrun -v -deffnm md_0_10 -cpi md_0_10.cpt -append -ntomp 4 Thank you. On Fri, Dec 28, 2018 at 12:12 PM Prasanth G, Research Scholar <