Hi Ross:
how nice it is for this coming amber version. I am even cannot help
to wait for it.
I am just wondering, will the CHARMM 36 would be available in this
new version? Since CHARMM36 is the best FF for nowadays main stream
lipids such as: POPE, POPC and so on. I've got a pieces of advices,
Desmond system builder tools is a very nice tool for membrane system
builder, and it will also improve a lot in the upcoming Schrodinger
based Desmond Version. Probably someone in Amber developer group can
consider make it comparable with the output from Desmond system builder
tool. As far as I know, the lipids name in from Desmond system builder
is different from standard CHARMM FF, but this problem would be fix in
the coming version.
Interesting, both Amber and Desmond will be released for their new
version this April. I am really looking forward to this special season.
best
Albert
On 02/28/2012 06:41 PM, Ross Walker wrote:
> 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 - 10:30:02 PST
