VMD-L Mailing List

From: Daniel Fellner (dfel694_at_aucklanduni.ac.nz)
Date: Wed Jul 22 2020 - 03:46:59 CDT

Hi all,

I'm using a fragment-based approach to parameterising a particularly large
molecule. I've already optimised the parameters for one fragment. Both
fragments share a common core indole moiety, so during the first fragment
parameterization some of the indole charges were optimized. When optimizing
the second fragment, should I update the PSF with the charges from the
previous fragment? Or leave them as the CGenFF-assigned (high penalty)
charges?

*Daniel Fellner BSc(Hons)*
PhD Candidate
School of Chemical Sciences
University of Auckland
Ph +64211605326