The structure of the chemokine receptor CXCR1 in phospholipid bilayers was released these days in Nature Letters. This is the first NMR GPCR structure and The receptor is in liquid crystalline phospholipid bilayers, without modification of its amino acid sequence and under physiologicalconditions. S ...
The Nobel Prize in Chemistry 2012 was awarded jointly to Robert J. Lefkowitz and Brian K. Kobilka "for studies of G-protein-coupled receptors (GPCR) http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2012/ Robert J. Lefkowitz Born: 194 ...
The recent CECAM workshop "High Performance Computing in Computational Chemistry and Molecular Biology: Challenges and Solutions Provided by ScalalLife Project" seems to be like Gromacs developer and users reunion meeting since it mainly focus on Gromacs and related topic. Lots of Gromacs guy ...
As the most important membrane protein, GPCR MD simulation is a quite hot topic nowadays. However, how to assemble protein/membrane system and which forcefield to assign for the whole system are two main critical and tough task for GPCR simulations. 1. Assemble protein/membrane system ...
As a highly optimized parallel MD tool, compiled Desmond is around 20-30% faster than the pre-compiled version which is distrubuted in Schrodinger software. here are some steps for how to compile Desmond from source code. 1. download source code from http://www.deshawresearch.com/resources_desmond. ...
---------------Restrain atoms --------------- restrain = { atom = "asl:(chain.name A) AND (atom.ptype CA)" force_constant = 10.0 } constraining protein CA or backbone is of great use when MD is producing based on homology models. ---------------Extract trajectory ----- ...
Installation: A) Install MPI. B) Make sure that the mpi compilers (mpicc?) are in the path visible to SCons; if they don't install to the standard place that the normal user can see, then you can try going into rosetta_source/tools/build and copying th ...
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