Re: [AMBER] GAFFlipid parameters

From: Dickson, Callum J <>
Date: Wed, 4 Jun 2014 12:52:44 +0000


Lipid14 is better able to reproduce NMR order parameters and X-ray scattering data - this data comes directly from experiment and does not require any modelling by the experimentalists (area per lipid, volume per lipid do however require modelling of the scattering data to extract these properties). We will also be continuing to update and support Lipid14, for example Ben's new script makes setting up membranes far easier (see tutorial 16).

All the best,

From: [] on behalf of []
Sent: 04 June 2014 13:24
To: AMBER Mailing List
Subject: Re: [AMBER] GAFFlipid parameters

   Dear Callum,

   thanks for your quick reply!

   As far as I know Lipid14 parameters are not correct to reproduce some
   parameters as,for example, volume per lipid. While GAFFlipid force field is
   good for calculation of volume and other parameters. So I think GAFFlipid
   force field 2012 is more suitable for use at the present time.

   I ask you to correct me if I'm wrong.

   Alexandra Antipina

   04.06.2014, 15:42, "Dickson, Callum J" <>:

     Hi Alexandra,
     I would suggest you use the updated Lipid14 parameters for POPC - these
     use (and have been tested with) the correct phosphorus angle parameters
     from gaff.dat.
     From: [1] [[2]] on
     behalf of áÎÔÉÐÉÎÁ áÌÅËÓÁÎÄÒÁ [[3]]
     Sent: 04 June 2014 10:01
     To: [4]
     Subject: [AMBER] GAFFlipid parameters
     Dear Amber Developers!
     I am working on MD simulations of POPC lipids. I would like to employ the
     GAFFlipid force field for simulations of POPC lipids with the use of the
     Gromacs package. I found the file with the force field parameters on the
     site [1][5] , but unfortunately this file
     not contain all parameters needed, and as far as I understood it serves as
     an additional file for the Amber package, so that the rest of parameters
     included in file gaff.dat of the Amber package. But as far as I know gaff
     parameters are constantly changing, for example, the parameters of P
     (phosphorus) for calculating the bond angle force constant. As I am not a
     user of the Amber package, it is difficult for me to identify which
     parameters were used for the development of your GAFFlipid force field in
     2012. I would be grateful if you helped me to obtain all the parameters of
     GAFFLipid force field for a POPC molecule.
     Alexandra Antipina
     Postgraduate student of Saint-Petersburg State University, Russia.
     1. [7]
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Received on Wed Jun 04 2014 - 06:00:05 PDT
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