Reply To: disulfid bonds

[kortemme]

Dear Forum readers
I’m trying to run a prediction with the connectivity of disulfide bonds that I know from experimental data. Please be so king to tell me how to do it if any of you know it. another question why do i need a pdb file to start with? (I’ve generated it by running with no fix_disulf first)

The things I´ve tried with no success were:

./rosetta.gcc aa –resfile –find_disulf –fix_disulf connectivity.cst –use_disulf_logfile –nstruct 1000

./rosetta.gcc aa –resfile resfilename.res –fix_disulf –use_disulf_logfile –nstruct 1000

./rosetta.gcc aa –resfile resfilename.res –find_disulf/fix_disulf –use_disulf_logfile –nstruct 1000

Been resfilename.ref generated with makeresfile modifying the Cys with the PIKKA flag

(makeresfile –p –resfile )

Many thanks