Re: Fatty Acid Topology

From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Mon Apr 02 2018 - 09:14:32 CDT

Probably you should use the CHARMM General Force Field for oleic acid. See:

https://cgenff.paramchem.org/

Jeff

–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
Website: http://jeffcomer.us

On Fri, Mar 30, 2018 at 9:25 PM, Nisler, Collin R.
<nisler.1_at_buckeyemail.osu.edu> wrote:
> 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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