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