Hi All,
I am trying to use AMBER18 to compute the hydration free energy of halogen substituted benzene with lone pairs. However, I can only get some information in section 17.7.4 of amber manual. In the manual, it says that the bonded terms are not computed with "frameon = 1" and only nonbonded (ele) terms will be computed.I have two questions to confirm in order to know how to prepare the input files (mol2 and frcmod) correctly:
1. how the position of the lone pair is determined from the input mol2 and frcmod files?
2. how does the lone pair evolve during MD simulations? Although in the manual it says "The lone pairs are kept in ideal geometry relative to local atoms, and resulting torques are transferred to these atoms", I still don't understand how it does in the code.
Any of your information about getting better understanding of this question is appreciated!
Thanks in advance!
Mingjun
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Received on Sat Mar 14 2020 - 08:00:02 PDT
