You can very easily prepare such systems with the nano material modeler from charmm-gui. You can prepare nano particles and surface models for most element and many compound materials.

https://www.charmm-gui.org/?doc=input/nanomaterial

The peptide can be build with several tools. VMD has the molefacture plugin:

https://www.ks.uiuc.edu/Research/vmd/plugins/molefacture/

I usually put the protein through charmm-gui (PDB Reader) and later join the pdb/psf pairs of nanoparticle and protein using the attached script. It expects two arguments, which are the names of the two molecules PSF/PDB files. For example if you have protein.psf and protein.pdb and nanoparticle.psf and nanoparticle.pdb you would type:

psfmerge protein nanoparticle

The program will call VMD and uses psfgen to join the molecules. Later you can solvate and ionize with VMD. Charmm-gui will give you also the parameter files for NAMD in the toppar folder. The parameter files for the solvent (toppar_water_ions_namd.str) I used from VMD.

Good luck ;)

charmm-gui has a problem and I did not suggest anyone to use if you really want to get a proper result, the problem is that when you generate your protein or the charmm-gui output you will find that charmm-gui has removed some amino acid inside the protein and add HSD, and you will find that occur in many places inside the sequence, that is a really serious error. if one mutation can change the MD result how we can accept the charmm-gui changing

Mohnad Abdalla I have never observed such problems you describe. It may had to do with a poorly prepared PDB file in your case. The charmm-gui is used very frequently throughout the MD community. If you have problems as serious as you described, you should file a bug report.

Norman Geist Mohnad Abdalla yes it changes the histidine name from HIS to HSD which is one of the protonation states of histidine in CHARMM36 forcefield. however, if you want a specific protonation state you can select in the second window that appears after uploading your file to CHARMM-GUI. but I have not seen it remove amino acids unless they have names that are not defined in the CHARMM36 force field. in this case, it asks you to either change its name (if left empty it will be removed) or upload a topology and parameter file for it

Norman Geist Thank you for these detailed steps. I tried to build a gold nanosphere using the CHARMM-GUI link you provided, but when I reached the final step of selecting the force field there was only one force field called INTERFACE. can I add it to the CHARMM36 force field files obtained when I build the system for the peptide?

Yes, the INTERFACE FF is considered compatible with the charmm protein forcefield.

Norman Geist Thank you for your help