You should follow the advice given to you on gmx-users: this is an extremely difficult system to deal with, one that has to be parametrized from scratch. Use of classical MD is unlikely to be useful here, but a QM approach like ab initio MD or DFT calculations are more likely to succeed. Parametrizing a ZnS nanosheet would take an experienced user considerable time to even prove that it's workable. Force field work is a very advanced topic, especially for something with physical properties that are unlikely to be modeled well with a classical force field.

What kind of interactions would you like to study between the mentioned fragments ?

i want to know how amino acid behave when encounter with sheet,for example its tendency to be adsorbed.

I suggest you to compare the free energy of the system in both presence and absence of the sheet.

thank you for your suggestion,but as I said I am a beginner and I think calculating free energy is such a hard work now,my question is that can I behave sheet as a ligand?

second challenge is that if you check the ZnS file that I attached in my first question,when I use any FF,I face with error:residue NU is not identified in force field database,what should I do ?

thank you

You should follow the advice given to you on gmx-users: this is an extremely difficult system to deal with, one that has to be parametrized from scratch. Use of classical MD is unlikely to be useful here, but a QM approach like ab initio MD or DFT calculations are more likely to succeed. Parametrizing a ZnS nanosheet would take an experienced user considerable time to even prove that it's workable. Force field work is a very advanced topic, especially for something with physical properties that are unlikely to be modeled well with a classical force field.

Hi Roja,

The following links may help you solve the 'residue not found in FF database' error.

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field?highlight=parameterization

https://www.researchgate.net/post/Gromacs_Residue_not_found_in_residue_topology_database_How_to_fix_this

Good luck. Let us know how you fixed it, when you do.