Software:Loopy DocumentationMod

From Honiglab_public

Using loopyMod:

loopyMod -prm num -obj num-num -seed num -ini num -cid char -out num -sec char -NmrStyle num file.pdb
-prm   force parameters. default 1
-prm 1: CHARMM22 with all atom model
-prm 2: AMBER with all atom model
-prm 3: CHARMM with heavy atom model
-prm 4: AMBER with heavy atom model
-obj num-num: start and end id of loops to be predicted
-seed num: random seed number
-ini: number of initial conformations generated.default is 1000
-cid: chain id. default is the chain with empty space
-out: number of outputs. default is 1
-res: sequence of the segment. optional.
-fast: fast mode. default is 1.
-fast 0: fast mode off.
-fast 1: fast mode on.
-NmrStyle 1: used only with closeg since no side chain information is provided.
-NmrStyle 2: will output the loops in a compact PDB NMR style format.
-closeseg 1:  uses a very fast implementation of Random Tweak to generate closed loops.
file.pdb   pdb file

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loopyMod is supported by a funding from the National Science Foundation Grant # MCB-0416708 and funding from the National Institute of Health Grant # GM30518.

Developed in the Honig Lab