Thank you very much sir!! I did discover why CGenFF server got confused based on your feedback. I manually adjusted the bond order earlier,and hence added the bond order of 2 for C=N and others accordingly. But I realized I should add "ar" in the bond order column since the pyridine system is a conjugated one. Updated mol2 file gave me CG2R62 for the C and others as I expected.

> Multiple parameter sets are often tested in simulations, so it is not unreasonable to test both choices and the CGenFF estimates.

Okay sir. I will test both types of parameters to evaluate them.

PLS-Ser does play an important role. Because of this, I did design a positive control and a negative control with our experimental collaborators to validate our simulation models.

Hopefully, through that I might be able to ensure the accuracy of the simulation setup (fingers crossed).

Thank you very much for your kind feedback (as always) on this.
Best,
Aravinda

Last edited by Aravinda; 07/14/19 12:47 AM.