[gmx-users] Membrane simulation with OPLS ff.

[Karthigeyan.Nagarajan at sanofi.com]

Thanks Justin.

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Justin Lemkul
Sent: Thursday, September 26, 2013 7:51 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Membrane simulation with OPLS ff.



On 9/26/13 10:47 PM, Christopher Neale wrote:
> Dear Karthi:
>
> As far as I am aware, there is no OPLSAA lipid force field. I have 
> used Berger lipids with OPLSAA protein ( 
> http://www.pomeslab.com/files/lipidCombinationRules.pdf ) but that is mixing a UA lipid with an AA protein so be aware of possible problems arising out of that.
>

There are OPLS-compatible lipids, though they are UA, but specifically designed to be used with OPLS-AA:

dx.doi.org/10.1021/ct900086b

I have not seen these parameters used very widely, though.

> Charmm has proteins and lipids, but charmm lipids require charmm tip3p 
> water (or at least tip4p or spc, certainly not regular tip3p) and are 
> thus slower to simulate in gromacs. I'm more recently using the Slipids (stockholm lipids) and Amber99SB-ILDN protein forcefield.
>

Solid choices.

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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