Re: [AMBER] GAFFlipid parameters

From: Dickson, Callum J <callum.dickson09.imperial.ac.uk>
Date: Wed, 11 Jun 2014 11:25:31 +0000

Hi Antipina,

The production runs used a 10 Å cut-off both for the electrostatics and the van der Waals, with the default AMBER analytical dispersion correction applied to treat van der Waals beyond the cut-off (so vdwmeth=1 as is the default).

Yes we are currently validating other lipids, including PS and PG lipids to release as an update.

All the best,
Callum

________________________________________
From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on behalf of Alexandra Antipina [aaju.yandex.ru]
Sent: 11 June 2014 10:35
To: AMBER Mailing List
Subject: Re: [AMBER] GAFFlipid parameters

   Thanks for the info, Callum!

   Ok, if Lipid14 is really better than GAFF, then I would also like to clarify
   some important details regarding the production run of lipid bilayer using
   Lipid14 parameters. I have read the paper âLipid14: The Amber Lipid Force
   Fieldâ , but I have not found some the cut-off radii for Van der Waals
   interactions and the cutoff scheme used for Van der Waals interactions.
   Therefore, I would be grateful if you could provide me with a simulation
   protocol you used for lipid.

   And another question:Â Should we expect Lipid14 for anionic lipids, such as
   POPS?

   Antipina Alexandra

   Â

   04.06.2014, 16:55, "Dickson, Callum J" <callum.dickson09.imperial.ac.uk>:

     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: [1]amber-bounces.ambermd.org [[2]amber-bounces.ambermd.org] on
     behalf of ÐнÑипина ÐлекÑандÑа [[3]aaju.yandex.ru]
     Sent: 04 June 2014 13:24
     To: AMBER Mailing List
     Subject: Re: [AMBER] GAFFlipid parameters
     Â Â Â Dear Callum,
     Â Â Â thanks for your quick reply!
     Â   As  far as I know Lipid14 parameters are not correct to reproduce
     some
     Â Â Â parameters as,for example, volume per lipid. While GAFFlipid force
     field is
     Â Â Â good for calculation of volume and other parameters. So I think
     GAFFlipid
     Â Â Â force field 2012 is more suitable for use at the present time.
     Â Â Â I ask you to correct me if I'm wrong.
     Â Â Â Alexandra Antipina
     Â Â Â 04.06.2014, 15:42, "Dickson, Callum J"
     <[4]callum.dickson09.imperial.ac.uk>:
     Â Â Â Â Â Hi Alexandra,
     Â Â Â Â Â I would suggest you use the updated Lipid14 parameters for POPC
     - these
     Â Â Â Â Â use (and have been tested with) the correct phosphorus angle
     parameters
     Â Â Â Â Â from gaff.dat.
     Â Â Â Â Â Cheers,
     Â Â Â Â Â Callum
     Â Â Â Â Â ________________________________________
     Â Â Â Â Â From: [1][5]amber-bounces.ambermd.org
     [[2][6]amber-bounces.ambermd.org] on
     Â     behalf of ÑâÑâÑâ Ñâ´ÑâÑâ´ÑâÑâ ÑâÑâÑâÑâÑâ ÑâÑâÑâÑâÑâ
     [[3][7]aaju.yandex.ru]
     Â Â Â Â Â Sent: 04 June 2014 10:01
     Â Â Â Â Â To: [4][8]amber.ambermd.org
     Â Â Â Â Â Subject: [AMBER] GAFFlipid parameters
     Â Â Â Â Â Dear Amber Developers!
     Â Â Â Â Â I am working on MD simulations of POPC lipids. I would like to
     employ the
     Â Â Â Â Â GAFFlipid force field for simulations of POPC lipids with the
     use of the
     Â Â Â Â Â Gromacs package. I found the file with the force field
     parameters on the
     Â Â Â Â Â site [1][5][9]http://lipidbook.bioch.ox.ac.uk/ , but
     unfortunately this file
     Â Â Â Â Â does
     Â Â Â Â Â not contain all parameters needed, and as far as I understood it
     serves as
     Â Â Â Â Â an additional file for the Amber package, so that the rest of
     parameters
     Â Â Â Â Â are
     Â Â Â Â Â included in file gaff.dat of the Amber package. But as far as I
     know gaff
     Â Â Â Â Â parameters are constantly changing, for example, the parameters
     of P
     Â Â Â Â Â (phosphorus) for calculating the bond angle force constant. As I
     am not a
     Â Â Â Â Â user of the Amber package, it is difficult for me to identify
     which
     Â Â Â Â Â parameters were used for the development of your GAFFlipid force
     field in
     Â Â Â Â Â 2012. I would be grateful if you helped me to obtain all the
     parameters of
     Â Â Â Â Â GAFFLipid force field for a POPC molecule.
     Â Â Â Â Â Alexandra Antipina
     Â Â Â Â Â Postgraduate student of Saint-Petersburg State University,
     Russia.
     Â Â Â Â Â [6][10]aaju.yandex.ru
     Â Â Â Â Â References
     Â Â Â Â Â 1. [7][11]http://lipidbook.bioch.ox.ac.uk/
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     References
     Â Â Â 1. mailto:[16]amber-bounces.ambermd.org
     Â Â Â 2. mailto:[17]amber-bounces.ambermd.org
     Â Â Â 3. mailto:[18]aaju.yandex.ru
     Â Â Â 4. mailto:[19]amber.ambermd.org
     Â Â Â 5. [20]http://lipidbook.bioch.ox.ac.uk/
     Â Â Â 6. mailto:[21]aaju.yandex.ru
     Â Â Â 7. [22]http://lipidbook.bioch.ox.ac.uk/
     Â Â Â 8. mailto:[23]AMBER.ambermd.org
     Â Â Â 9. [24]http://lists.ambermd.org/mailman/listinfo/amber
     Â Â 10. mailto:[25]AMBER.ambermd.org
     Â Â 11. [26]http://lists.ambermd.org/mailman/listinfo/amber
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References

   1. mailto:amber-bounces.ambermd.org
   2. mailto:amber-bounces.ambermd.org
   3. mailto:aaju.yandex.ru
   4. mailto:callum.dickson09.imperial.ac.uk
   5. mailto:amber-bounces.ambermd.org
   6. mailto:amber-bounces.ambermd.org
   7. mailto:aaju.yandex.ru
   8. mailto:amber.ambermd.org
   9. http://lipidbook.bioch.ox.ac.uk/
  10. mailto:aaju.yandex.ru
  11. http://lipidbook.bioch.ox.ac.uk/
  12. mailto:AMBER.ambermd.org
  13. http://lists.ambermd.org/mailman/listinfo/amber
  14. mailto:AMBER.ambermd.org
  15. http://lists.ambermd.org/mailman/listinfo/amber
  16. mailto:amber-bounces.ambermd.org
  17. mailto:amber-bounces.ambermd.org
  18. mailto:aaju.yandex.ru
  19. mailto:amber.ambermd.org
  20. http://lipidbook.bioch.ox.ac.uk/
  21. mailto:aaju.yandex.ru
  22. http://lipidbook.bioch.ox.ac.uk/
  23. mailto:AMBER.ambermd.org
  24. http://lists.ambermd.org/mailman/listinfo/amber
  25. mailto:AMBER.ambermd.org
  26. http://lists.ambermd.org/mailman/listinfo/amber
  27. mailto:AMBER.ambermd.org
  28. http://lists.ambermd.org/mailman/listinfo/amber
  29. mailto:AMBER.ambermd.org
  30. http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Jun 11 2014 - 04:30:02 PDT