Hi Cody,
I'd be careful before proceeding with this project. ff12SB is a fixed charge protein and nucleic force field that is a part of AmberTools 12.
Indeed, GAFF was a starting point for lipid force field parameterization in GAFFlipid and Lipid11. Let's say you have a new glycerophospholipid that has two tails like those in GAFFlipid (Myristoyl, lauroyl, palmitoyl, oleoyl). In principle, you can use the atom types and updated GAFFlipid parameters (van der Waals and dihedrals) for the tails in your new glycerophospholipid. For most of the head groups we've worked with, we've used the GAFF parameters as a basis for the head group parameters. In some cases with sugars, we've additionally combined Glycam parameters as well.
The challenging part however will be to re-examine and possibly refit the dihedrals of the head group, as well as obtain partial charges for the entire phospholipid. The GAFFlipid paper explains in detail the way that dihedral scans were compared with QM energies, and goes into depth about the charge derivation approach.
We've been working on an update to GAFFlipid and Lipid11 that will make the problem you face much easier. What type of phospholipid are you interested in parameterizing?
All the best,
Ben Madej
Walker Molecular Dynamics Lab
________________________________________
From: Ganesh Kamath [gkamath9173.gmail.com]
Sent: Monday, April 15, 2013 11:32 AM
To: AMBER Mailing List
Subject: Re: [AMBER] GAFFlipid using custom lipids
What types of lipids are you trying to simulate. If you tell the names,
maybe people can help.
On Mon, Apr 15, 2013 at 1:23 PM, Covington, Cody Lance <
cody.l.covington.vanderbilt.edu> wrote:
> Hello
>
> I want to simulate a lipid not used in the paper by CJ Dickson, L Rosso,
> RM Betz, RC Walker, IR Gould - Soft Matter, 2012.
> Since the parameterization for GAFFlipid only changed the interactions in
> the tail, shouldn't I be able to use ff12SB and GAFF to handle the head
> group and use GAFFlipid for the tail?
>
> Thanks
> Cody
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 15 2013 - 12:30:02 PDT
