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

March, 2012; Michelle Sahai, Ph.D., a Postdoctoral Associate in Harel Weinstein's lab, was awarded a three year Canadian Institutes of Health Research (CIHR) Fellowship for her research on Molecular Mechanisms of the Dopamine Transporter Function: The effects of drugs of abuse.
Feb, 2012; Sayan Mondal, a student in Harel Weinstein's lab, won the Student Research Achievement Award at the Biophysical Society's 2012 Annual Meeting for his poster on the interaction of GPCRs with the membrane.
Jan, 2012; Jan Dlabal, a student from the Lycée Français de New York, was selected as a semi-finalist in the 2012 Intel Science Talent Search, for work on the determination of large-scale genomic structure performed in the lab of Olivier Elemento.
Oct, 2011; Sheila Nirenberg presented a talk, "Can we speak the language of the brain?", at the TEDMED 2011 conference. A Q & A session followed.
Nov, 2011; GobyWeb binary release. The Campagne laboratory has just released a binary distribution of GobyWeb. This first public release of GobyWeb makes it possible to install the tool locally for non-commercial use. Detailled installation instructions are available on the download page.
Apr, 2011; Dr. Olivier Elemento was awarded an NSF CAREER Grant, the National Science Foundation's most prestigious award in support of junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education and the integration of education and research.
Nov, 2010; Dr. Sheila Nirenberg's work on artificial retinas has been featured in Technology Review, Wired, Scientific American, and the New Scientist.
Jul, 2009; ChIPseeqer, a comprehensive framework for analysis of ChIP-seq data developed in the Elemento lab, is now available for download. [More]

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