Hi all,

I am trying to set up an MD simulation of a nanoporous MoS2 membrane in GROMACS. I generated the nanosheet structure from CHARMM-GUI and tried to introduce a nanopore by deleting atoms in a cylindrical zone from the original pdb. Now I am struggling to create the topology file for this. I tried ParmEd and MD analysis modules and have not yet been completely successful. Could anyone suggest a way to generate the topology for an edited pdb file?

I tried using vmd to generate psf file. I am attaching the tcl script below along with the output. Now the problem is that vmd generated output is not consistent with the input files. There are additional atoms printed in the pdb and psf whcih has coordinate zero! Could anyone suggest a way to solve this?

Thanks

Pragin