Fatty Acid Topology

From: Nisler, Collin R. (nisler.1_at_buckeyemail.osu.edu)
Date: Fri Mar 30 2018 - 21:25:30 CDT

Hello, I am interested in simulating an all atom membrane that includes single chain fatty acid molecules, particularly oleic acid. I know top_all27_prot_lipid.rtf included oleic acid, but it is my understanding that it was problematic, in addition to the fact that the current topology for CHARMM36 does not include fatty acids. Is it advisable to create an oleic acid topology file by taking a portion of the POPC model from top_all36_lipid.rtf (in particular the oleyol chain) and adding an appropriate patch to the end to capture the carboxyl group? Thanks very much.

Collin Nisler

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