Hi all,
I am new to computational field. currently, am working in protein-protein interaction. Is it necessary that we have to apply forcefield before docking and once i am applying forcefield, i am seeing the following error,
After navigating to the simulation tab, I proceeded to choose the Forcefield option. Then, I clicked on Charmm27 and applied the selected forcefield. "The following residues do not have a template: A:ACE0, A:HYP2, A:HYP5, A:HYP8, A:HYP23, A:HYP26, A:HYP29, B:HYP2, B:HYP5, B:HYP8, B:HYP23, B:HYP26, B:HYP29, C:ACE0, C:HYP2, C:HYP5, C:HYP8, C:HYP23, C:HYP26, C:HYP29."
Kindly suggest me to rectify this.
Thanks
Nithya, Long Island University
What software are you using?
From the error, it is evident that you want to run MD simulation, and the system is not parametrized. You need to generate parameters for different residues in chain A-C such as ACE0, HYP5 etc. Once, you have created these, then the simulation will proceed.
Assignment of force field parameters is essential step in any molecular modelling calculations. All the calculations are carried out using these parameters. From the error, it looks like that parameters/topology file for the indicated residues are in not available in CHARMM force field library. Given residue name are not canonical residue and hence their parameters have to be generated and appended as suggested by Dr Ayaz.