Hi Albert,
> thanks a lot for your kind messages. I am wondering will the issue
> for
> membrane protein as David A Case mentioned be solved in the upcoming
> new
> version ?
AMBER 12 (Sander, PMEMD and PMEMD.cuda) will support constant surface
tension NPgammaT calculations, in the XY, XZ or YZ planes as has been used
in the past for the Charmm ALL27 force field. Using Chamber you will thus be
able to run lipid simulations using the Charmm force field in AMBER 12. It
will also include a new phospholipid force field termed Lipid11 (The
manuscript is currently in review) that is designed to be compatible with
the AMBER FFxx, Glycam and GAFF force fields. However, this is the first
generation of this Lipid force field and so mileage may vary. There will not
be any specific tools for setting up lipids you will be expected to provide
PDB files in the correct format for processing by Leap and/or Chamber.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Tue Feb 28 2012 - 10:00:02 PST
