GROMACS modification: Yes/No
Hello Everyone,
I have been trying parameterize a small part of a bigger molecule(91 atoms), which have a charge penalty of 25 and dihedral penalty of 45.
I understand that these relatively high penalties indicate that the corresponding parameters should be validated/re-optimized rather than used blindly.
I initially tried to optimize the parameters using the fftk+ORCA workflow at the MP2 level. However, I am having difficulty obtaining good convergence between the QM and MM energies.
I went through the charmm36 parameter files and found that the dihedral I have a high penalty is available in the carbohydrate parameter file(a similar chemical environment). Would it be reasonable to use the existing CHARMM36 carbohydrate dihedral parameter as the starting value for optimization/validation, provided that the local chemical environment is sufficiently similar?
There is also another issue. When I use the CGenFF-generated topology directly in GROMACS, I obtain extremely large potential-energy values for the molecule.
Would ffParam be a better option for parameter optimization in this case, or would you recommend continuing with the ffTK + ORCA workflow?
I would appreciate any kind of help and advice on how to tackle the parameterization and validation.
Thank you,
Asha