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: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on behalf of Антипина Александра [aaju.yandex.ru]
Sent: 04 June 2014 10:01
To: 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]
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.
aaju.yandex.ru
References
1.
http://lipidbook.bioch.ox.ac.uk/
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Received on Wed Jun 04 2014 - 05:00:03 PDT
