Re: Fatty Acid Topology

From: Fotis Baltoumas (fbaltoumas_at_biol.uoa.gr)
Date: Mon Apr 02 2018 - 12:46:54 CDT

Hello Collin,

Actually, oleic acid, alongside other detergents, is included in
CHARMM36.  If you download the latest C36 parameters from Mackerell's
lab (http://mackerell.umaryland.edu/charmm_ff.shtml#charmm ), you can
find it in the "toppar_all36_lipid_detergent.str" stream file, in the
"toppar/stream/lipid" directory.  Oleic acid is named "OLE".

Fotis

On 04/02/2018 05:14 PM, Jeff Comer wrote:
> 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

-- 
*******************************************
Fotis A. Baltoumas
Bioinformatics Postgraduate Programme
Section of Cell Biology and Biophysics
Department of Biology, National & Kapodistrian University of Athens
Panepistimiopolis, Athens 157 01, GREECE
   --------------------------------------
email : fbaltoumas_at_biol.uoa.gr
http://biophysics.biol.uoa.gr
http://bioinformatics.biol.uoa.gr
*******************************************

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