On Wed, Feb 5, 2014 at 9:14 AM, Gözde YALÇIN <yalcingozde88.gmail.com>wrote:
> Hi,
>
> I would like to implement a MD simulation of a protein embedded in a
> POPC+POPE+Cholesterol lipid bilayer. I was able save a pdb for the entire
> system. I was wondering if it is possible to parameterize lipid part of
> the system in leap using charmm force field. If so, does anyone please let
> me know of how to do that?
>
Hannes's suggestion is good if you want to parametrize your entire system
using the CHARMM force field. However, if you want to do the lipid part
with CHARMM and the rest with Amber, there is no way to do this. In my
opinion, this is a Good Thing, since there's no reason to believe that such
a combination would work 'well' together in the first place (different
charge derivation and parametrization scheme, as well as different
functional forms for the force field).
I would suggest either using the Lipid14 force field (recently published
and released on this mailing list in the past couple weeks) to do the whole
thing with Amber-compatible force fields or to parametrize everything with
CHARMM and convert to Amber topologies if you want to use Amber MD engines.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 05 2014 - 08:30:02 PST
