Cody,
OK, I see what you mean about ff12SB for the head group. I have not tried any phospholipids with that kind of head group and I'll look into it. It's a good question about how transferable the parameters for the phenylalanine from ff12SB would be for a phospholipid head group. There are others on the mailing list who have much more insight into the history of ff12SB and the Amber protein force fields than I do.
That is interesting that RED provides a net charge of about 0.4e for the tail. My question is what sort of lipid system is this? Is it a monolayer or bilayer type system that you're investigating, or some other polymer? Your approach may vary based on the type of system. Lipid11 does use a capping and RESP charge derivation scheme specific for phospholipids and we've been looking at several strategies for lipid partial charge derivation.
Ben
Walker Molecular Dynamics Lab
________________________________________
From: Covington, Cody Lance [cody.l.covington.Vanderbilt.Edu]
Sent: Monday, April 15, 2013 12:52 PM
To: AMBER Mailing List
Subject: Re: [AMBER] GAFFlipid using custom lipids
Ben
> What type of phospholipid are you interested in parameterizing?
I am actually doing a surfactant that is the dodecyl ester of phenylalanine, so the head is a phenylalanine, with a protonated nitrogen(very different from your lipids).
Could you advise the best force field to use for this head group? Should I use ff99SB and GAFF or something else?
> 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.
I have tried the REDs server using the entire molecule and a +1 charge, but I gives a net charge on the "tail" of about 0.4 e. I think this is a large charge for a carbon chain, so I was going to use a 2 part charge fitting described in the Lipid11 paper and compare results. Does this sound reasonable?
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
Received on Mon Apr 15 2013 - 15:30:02 PDT
