Hi folks,
This is an advance announcement for (1) an AMBER developer job opening and
(2) a postdoc opening for a position to develop and carry out FEP/TI
calculations using Cando (more info below) and AMBER.
We are seeking people to fill two positions:
(1) A software developer with experience in C++ and Python programming and
a willingness to learn other languages (specifically Common Lisp - Cando's
high-performance scripting language). Experience with AMBER and carrying
out molecular dynamics and FEP/TI calculations is also important. This
person will be developing Cando, using Cando and interfacing with drug
companies who are interested in using Cando for drug discovery.
(2) A postdoc position in computational chemistry. This person will carry
out FEP/TI calculations and develop computational chemistry tools within
Cando.
This person will interact with a software development group at Temple
University, ThirdLaw LLC, computational chemistry groups at other
Universities and at drug discovery companies.
Cando is a powerful new software tool developed by the Schafmeister group,
and being commercialized by ThirdLaw LLC, to carry out advanced FEP/TI
calculations and more generally to facilitate the process of computer-aided
molecular design. Cando is open source and freely available at
https://github.com/cando-developers/cando.git. Cando development is
supported for the next two years by a DOE Phase II STTR grant.
Cando...
- is open source: https://github.com/cando-developers/cando.git
- is a command line application.
- has a Jupyterlab, web based, client/server based UI for designing
molecules.
- is a drop in replacement for "tleap" and most of the AmberTools with
greatly enhanced capabilities.
- is a programming environment with a powerful C++ library for manipulating
molecules, model building, preparing simulations (currently AMBER, more
with time) and analyzing simulations.
- has a compiler that generates fast native code using the LLVM library,
including an integrated IDE and debugger.
- interoperates with C++ libraries.
- implements the AMBER/GAFF toolchain.
- generates AMBER topology files.
- reads all AMBER file formats and many others.
- implements SMARTS/SMIRKS pattern matching.
- implements the SMIRNOFF force-field.
- has a Python3 bindings.
- has an internet distribution system for distributing Cando applications
that are installed and compiled by the user with a single command.
- incorporates a free energy perturbation setup application that uses AMBER
as the molecular dynamics engine.
Christian Schafmeister,
Founder ThirdLaw LLC,
Professor, Chemistry Department,
Temple University
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Received on Thu Aug 08 2019 - 10:30:05 PDT
