Hi,
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 charmmlipid2amber.py script makes setting up membranes far easier (see tutorial 16).
All the best,
Callum
________________________________________
From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on behalf of [aaju.yandex.ru]
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" <callum.dickson09.imperial.ac.uk>:
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.
Cheers,
Callum
________________________________________
From: [1]amber-bounces.ambermd.org [[2]amber-bounces.ambermd.org] on
behalf of áÎÔÉÐÉÎÁ áÌÅËÓÁÎÄÒÁ [[3]aaju.yandex.ru]
Sent: 04 June 2014 10:01
To: [4]amber.ambermd.org
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]
http://lipidbook.bioch.ox.ac.uk/ , but unfortunately this file
does
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
are
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.
[6]aaju.yandex.ru
References
1. [7]
http://lipidbook.bioch.ox.ac.uk/
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[9]
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[10]AMBER.ambermd.org
[11]
http://lists.ambermd.org/mailman/listinfo/amber
References
1. mailto:
amber-bounces.ambermd.org
2. mailto:amber-bounces.ambermd.org
3. mailto:
aaju.yandex.ru
4. mailto:amber.ambermd.org
5.
http://lipidbook.bioch.ox.ac.uk/
6. mailto:aaju.yandex.ru
7.
http://lipidbook.bioch.ox.ac.uk/
8. mailto:
AMBER.ambermd.org
9.
http://lists.ambermd.org/mailman/listinfo/amber
10. mailto:AMBER.ambermd.org
11.
http://lists.ambermd.org/mailman/listinfo/amber
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AMBER mailing list
AMBER.ambermd.org
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Received on Wed Jun 04 2014 - 06:00:05 PDT
