Re: [AMBER] GAFFlipid parameters

From: <aaju.yandex.ru>
Date: Wed, 04 Jun 2014 16:24:17 +0400

   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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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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Received on Wed Jun 04 2014 - 05:30:03 PDT
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