SimRNA (c) 2009-2024 Genesilico, ver. 3.33

PDB
/home/simrnaweb/SimRNAWeb/libs/SimRNP/SimRNP: unrecognized option '--dist-restr'
===================================SimRNA========================================


To run simulation with SimRNP you can use the following options:

----------------------------Obligatory Options-----------------------------------

	-N  or --run-name <string>: a name for the run, any character is acceptable.
Choose an appropriate option from the below as starting point for your simulation.
	-s or --seq <path to seq file>: starting from a sequence file
	(the initial conformation is a circle).
	-p or --pdb <path to pdb file>: starting from a pdb file
	(good if you could find the homolog struture).
	-P or --PDB <path to pdb file>: starting from a pdb file
	(good for refinement, it restrict the movement of each nucleotide with their occupancy and bfactor).

-----------------------------Optional Options------------------------------------

	-c or --config [path to config file]: configuration for the simulation
	(you can use the one provided by us, 'config.dat').
	-R or --random-seed [integer number]: for generating same results.
	-o or --output [output name]: a name for the output (default: run-name).
	-S or --str-restr-slope [path to restraints file]: using the inforamtion for initializing structure restraints
	(it will apply slope restraints).
	-W or --str-restr-well [path to restraints file]: using the inforamtion for initializing structure restraints
	(it will apply well restraints).
	-d or --distance-restr [path to restraints file]: using the inforamtion for initializing distance restraints.
	-C or --chem-restr [path to chemical probing restraints file]: using reactivity of each nucleotide and compare it with predicted SS in each frame.
	-T or --prot-ss-restr [path to protein SS restraints file]: using the information for initializing SS restraints on protein.
	-t or --trc-rescoring [path to trc and hdr file seperated by space]: rescore the sequence with conformations in the provided trc file.
	-E or --replicas [integer number]: swith on replica exchange method
	(argument indicates the number of replicas).
	-n or --n-iterations [integer number]: indicating the number of iterations for the simulation.
	-i or --interface
	-l or --write-pdb-ss: the software will write pdb format file and ss file for each frame of the simulation.
	-h or --help: to show the help menu