How do I run ICDA to produce an all-atom structure of a protein?

I read about ICDA (Independent Cluster Decomposition Algorithm) in these two papers: The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling, Jianing Li, Robert Abel, Kai Zhu, Yixiang Cao, Suwen Zhao, Richard A. Friesner, Proteins: Structure, Function, and Bioinformatics. and Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling Xin Li, Matthew P. Jacobson, Kai Zhu, Suwen Zhao, Richard A. Friesner Proteins: Structure, Function, and Bioinformatics, 2007, 66 (4), 824-837

Set up a side-chain prediction job in Prime (Applications → Prime → Refinement), write the input file, edit the input file to change PRIME_TYPE to ICDA, and then run the job from the command line using the command:

$SCHRODINGER/refinestruct input-file.inp

Here is what the input file should look like:

STRUCT_FILE input-file.mae
JOB_TYPE REFINE
PRIME_TYPE ICDA
SELECT all
NUM_SC_OUTPUT_STRUCT 1
USE_CRYSTAL_SYMMETRY no
USE_RANDOM_SEED no
SEED 0
EXT_DIEL 80.00
USE_MEMBRANE no
HOST localhost


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