[gmx-users] POPC Berger lipids parameters for AMBER99sb

[Carlos Navarro]

Dear Justin,
Thanks for the reply.
I forgot to mention that indeed the reason of using Berger lipids is
because there are united-atom. I'm planning on running computational
electrophysiology simulations, and since my system is about 600k atoms I
want to use vsites, as De Groot has been doing recently
https://www.nature.com/articles/s41467-018-03179-y
Best regards,
Carlos

On Tue, Jul 9, 2019 at 1:50 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/8/19 7:31 PM, Carlos Navarro wrote:
> > Dear gmx-users,
> > I was wondering if someone can share the Berger parameters for POPC for
> > Amber99sb (and I they can share also a .pdb .gro file will be even
> better).
> > I found several for gromos, but I need them form AMBER99sb.
>
> Berger parameters are united-atom and designed for use with GROMOS. I
> know some people have combined them with various protein force fields
> with varying success, but I would not do that. Berger parameters are
> wildly outdated and much better force fields exist. In your case, use
> Slipids, which are specifically designed to be compatible with AMBER.
>
> -Justin
>
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-- 

----------

Carlos Navarro Retamal

Bioinformatic Engineering. PhD

Postdoctoral Researcher in Center for Bioinformatics and Molecular
Simulations

Universidad de Talca

Av. Lircay S/N, Talca, Chile

T: (+56) 712201 <//T:%20(+56)%20712201> 798

E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl