Dear Readers,
I have been trying to use the pepspec application /main/source/bin/pepspec.linuxgccrelease @xyz.options with following as the contents of .options file
-in:file:s letssee.pdb
-pepspec:pep_anchor 90
-pepspec:pep_chain A
-pepspec:n_prepend 0
-pepspec:n_append 0
-pepspec:n_peptides 100
I am sure I am mkaing a mistake and it would be great if someone can guide me to write an options file for denovo docked peptide optimization with 10 N terminal and 10 C terminal appendin residues.
I would also like to know how rosseta identifies which peptide to choose out of the two docked proteins in the input structure and what if we have more than 1 residue that we would like to be keep constant (pep_anchor) during the design in the docked peptide.
Thanks alot
Best,
Neeraj Gaur
HI There,
I am trying to run pepspec_anchor_docking and get the following erros:
pepspec_anchor_dock.cc: line 1: //: is a directory
pepspec_anchor_dock.cc: line 1: tab-width:2: command not found
pepspec_anchor_dock.cc: line 1: indent-tabs-mode:t: command not found
pepspec_anchor_dock.cc: line 1: show-trailing-whitespace:t: command not found
pepspec_anchor_dock.cc: line 1: rm-trailing-spaces:t: command not found
pepspec_anchor_dock.cc: line 2: //: is a directory
pepspec_anchor_dock.cc: line 3: //: is a directory
pepspec_anchor_dock.cc: line 4: syntax error near unexpected token `c'
pepspec_anchor_dock.cc: line 4: `// (c) Copyright Rosetta Commons Member Institutions.'
Can any one help wiht this?