From: Yuvam Bhateja (
Date: Tue Oct 06 2020 - 11:17:26 CDT

Hello experts.

I am new to VMD and Molecular Dynamics.

I want to build a ligand coated silver nanoparticle. I do not want to go
into atomistic calculation and need the composite structure for a coarse
grained calculation later.
I think the structure needs to be simulated in water.

Can someone please help what all input files I need and a step by step
procedure for constructing these files?
I have build my nanoparticle and obtained the ligand separately.
How can I reduce the no of Atoms in ligand? I obtained it from RCSB PDB.

I'll be highly obliged for any help or guidance.

Yuvam Bhateja