Structure Calculation Using CS-Rosetta

Structure Calculation with CS-Rosetta

Original Documentation

http://spin.niddk.nih.gov/bax/software/CSROSETTA/index.html

Random Coil Index Prediction

Perform flexible region prediction on the RCI Web Page.

RCI will take a bmrb file in the old format, as produced by CYANA 1.0 (the new BMRB format has an extra "chain" column). Unlike AutoStructure input file, the sequence field should be left in place.

Use an init.cya file: name:=XXXX # Replace XXXX with NESG ID cyanalib # Read the standard library pseudo=2 # Allows HB, HD, etc. pseudoatom names, use with CARA read seq $name # Initialize

If you are using proton list from CARA, convert it first to "dyana" format with Cyana 2.1: read prot XXXX.prot pseudo=0 translate dyana write prot XXXX_dyana

Use cyana 1.0.5 to prepare a bmrb file read prot XXXX_dyana.prot bmrblist XXXX.bmrb

Make sure you change the _Chem_shift_ambiguity_type tag to _Chem_shift_ambiguity_code. Yes, it is stupid, but RCI will report an error if you don't do it.

Flexible N- and C-terminal tails should be removed for CS-ROSETTA calculation to reduce CPU time. Flexible loop regions will later be excluded from calculation of all-atom energy.

Generating MFR fragments on U2 cluster at SUNY Buffalo

Copy the runCSRjob.com file into the working directory and change the number of fragments to be generated.

Type qsub runCSRjob.pbs to submit the job into queue. This calculation takes ~2 hours for 1000 fragments for a small protein, therefore it cannot be run on a master node.

Running CS-Rosetta on U2 cluster at SUNY Buffalo

Go to the rosetta subdirectory. Figure out how many parallel Rosetta jobs you will need to run. Things to consider are:

• The total number of fragments to be calculated
• The maximum wall-time for a single job is 72 h
• It takes ~10 min to calculate a single structure of a small protein on a single CPU

Type ./runRosetta.csh N, where =N= is the number of parallel Rosetta jobs

-- Main.AlexEletski - 17 Apr 2008