Re: Fatty Acid Topology

From: Brian Radak (brian.radak_at_gmail.com)
Date: Sun Apr 01 2018 - 09:01:48 CDT

NAMD will accept most force fields in CHARMM /Xplor and Amber format. You
can use psfgen to construct Xplor PSFs from topologies in CHARMM RTF format
(like the one you describe). More fully featured tools are available with
VMD, but you'd have to direct your question to that list.

Aside from that the code makes no comments on the quality or usefulness of
the force fields - you'll have to check the literature on that.

HTH,
BKR

On Fri, Mar 30, 2018, 10:27 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
>

This archive was generated by hypermail 2.1.6 : Sat Sep 21 2019 - 23:19:28 CDT