Re: [AMBER] DMPG lipid bilayer simulations?

From: Dickson, Callum J <>
Date: Thu, 11 Sep 2014 13:23:32 +0000

Hi Jarrod,

We are currently validating parameters for anionic lipids, including PG lipids, which will be released once properly tested. So yes there is a plan to release PG, PS parameters in the near future.

It would be straight-forward to run DMPG just now with a combination of lipid11 and lipid14 force fields (as you say load them both into leap) and these are the parameters I started with when working on PG, however I found the bilayer to be too gel phase like at 303K. So this combination of parameters does not suitably represent PG lipid types.

From: Smith, Jarrod A [jarrod.smith.Vanderbilt.Edu]
Sent: 04 September 2014 21:28
Subject: [AMBER] DMPG lipid bilayer simulations?

Hi all,

Wondering if this is possible now or in the near future? The situation is that we have MY residues only in Lipid14 and PG residues only in Lipid11. Will PG be forthcoming in Lipid14? I think I there was a comment in the lipid tutorial that the old residues would be moved over as time permits. Can we get some guidance on that?

In the meantime, can we construct "chimera" lipids from the two different lipid forcefields or will Bad Things happen? If that sounds viable to the experts, could I please get a brief outline on a procedure to do that? i.e. can we load both forcefields into LEaP at the same time, or???



Jarrod A. Smith, Ph.D.
Asst. Director, Center for Structural Biology
Research Assoc. Professor, Biochemistry
Vanderbilt University - 5135 MRB III
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Received on Thu Sep 11 2014 - 06:30:02 PDT
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