institute for computational biomedicine: AMBER

[ description ]

AMBER refers to two things: it is both a suite of programs for carrying out molecular dynamics simulations, particularly on biomolecules, and a set of molecular mechanical force fields.

[ documentation ]

The AMBER 7 user's manual is available in PDF format from the AMBER web site. A series of AMBER tutorials is available from the same site.

[ availability ]

A serial version of AMBER 7 is available on all IRIX computers, and on osiris.
After you have configured your account to use WMC login scripts, you can use the sander and other AMBER commands at the UNIX command prompt.

Examples:

$ nucgen -O -i nuc.in \
-o nuc.out \
-d $AMBERHOME/dat/leap/parm/nucgen.dat \
-p nuc.pdb

$ sander -O -i fixit.in \
-o fixit.out \
-c polyAT_vac.inpcrd \
-p polyAT_vac.prmtop \
-r fixit.restrt -ref polyAT_vac.inpcrd

$ ambpdb -p polyAT_vac.prmtop < fixit.restrt > fixit.pdb

News

Jul, 2009; ChIPseeqer, a comprehensive framework for analysis of ChIP-seq data developed in the Elemento lab, is now available for download. [More]
Apr, 2009; The BDVal program developed by the Campagne laboratory for MAQC-II is now available from http://bdval.org. The software supports the development and evaluation of predictive biomarker models from high-throughput data. The web site offers binary and source distributions. [More]

[News Archives] [Mailing List]

Events

Feb 12th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Emre Aksay; ICB Conference Room - Y.1301
Mar 12th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Olivier Elemento; ICB Conference Room - Y.1301
Apr 9th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Christopher E. Mason; ICB Conference Room - Y.1301