PEPSPEC – Rosetta Commons

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- January 3, 2018 at 10:24 am #2824
  Anonymous
  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
- July 8, 2020 at 11:44 am #15371
  Anonymous
  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?
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