CRT home > 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
July, 2014; Mike LeVine, a PBSB graduate student in Harel Weinstein's lab, received a Best Poster Award at the 3DSIG2014 Structural Bioinformatics and Computational Biophysics meeting for his poster entitled "NBIT: An N-body information theory framework for understanding collective motions in proteins".
Sept, 2013; Dr. Sheila Nirenberg was awarded a MacArthur Fellowship for her work on how the brain encodes visual information.
Aug, 2013; Christopher E. Mason, Assistant Professor in Physiology and Biophysics, received an Excellence in Partnering award from the Centers for Disease Control and Prevention Agency for Toxic Substances and Disease Registry for "exemplary contributions to a framework for quality laboratory integration of genome sequencing technologies into healthcare delivery."
Apr, 2013; Christopher E. Mason, Assistant Professor in PBSB Program, was featured in Reuters, Nature, Newsday, CBC news, Huffington Post, The New Yorker, The Washington Post, and other media outlets for his recent paper on gene patents published in Genome Medicine and also for his work as a scientific expert on gene patents for the AMP v. Myriad Genetics case before the US Supreme Court.
Apr, 2013; Sheng Li, a PBSB graduate student in Dr. Christopher E. Mason's lab, won a National Science Foundation Travel Fellowship and was invited to give a speech at the 17th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2013) held at the Tsinghua University for her paper on "An optimized algorithm for detecting and annotating regional differential methylation".
Mar, 2013; Two Graduate Students working with PBSB faculty were awarded competitive graduate research fellowships: (1) Lenore Pipes, a graduate student in the Tri-Institutional Graduate Program in Computational Biology and Medicine, working in the laboratories of Dr. Christopher E. Mason and Dr. Adam Siepel, won a 2013 National Science Foundation (NSF) Graduate Research Fellowship Program (GRFP) Fellowship for her work on de novo transcriptome assembly and genome assembly. Her fellowship will last from 2013-2016. (2) Michael LeVine, a PBSB graduate student working in the lab of Dr. Harel Weinstein was awarded a National Research Service Award (NRSA - F31) to work on "Ligand-Specific Allosteric Modulation by Drugs of Abuse" for the next 4 years, starting June 1, 2013.
Jan, 2013; Dr. Olivier Elemento was awarded a five-year Irma T. Hirschl Career Scientist Award.
Dec, 2012; Mr. Vaja Liluashvili, a visiting graduate student in the Gumus laboratory was awarded a Sao Paulo Research Foundation (FAPESP) full fellowship to present at the international meeting SPAS: Advances in Molecular Oncology: Translating Molecular Biology into Cancer Treatment in Sao Paulo, Brazil 3-8th February 2013. Mr. Liluashivili will present his research with Dr. Zeynep H. Gumus, titled "iCAVE: immersive 3D visualization of complex biomolecular interaction networks".
Sept, 2012; The Campagne laboratory was awarded the best poster award for "Compression of high-throughput sequencing data" at the Wellcome Trust's Genome Informatics 2012 meeting in Cambridge, UK.
May, 2012; Dr. Christopher Mason was featured in a two part profile by the New York Genome Center for his work on non-human primate genomics, gene patenting policy, and other activities.
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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