Hi Albert
> 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.
Charmm 36 should already be supported. It is possible Chamber might need
some tweaks to be able to read the charmm psf and par / top files correctly
if they messed with the format but it should be working. I haven't heard any
major complaints. The thing that is missing from AMBER 11 is the constant
surface tension terms but 'supposedly' these are not needed for All36 so you
should be able to run that fine in AMBER 11 if you build yourself a psf.
As for naming it should be possible to script for that fairly easily.
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 - 14:00:02 PST
