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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


Neeraj Gaur

Post Situation: 
Wed, 2018-01-03 02:24

HI There,


I am trying to run pepspec_anchor_docking and get the following erros: line 1: //: is a directory line 1: tab-width:2: command not found line 1: indent-tabs-mode:t: command not found line 1: show-trailing-whitespace:t: command not found line 1: rm-trailing-spaces:t: command not found line 2: //: is a directory line 3: //: is a directory line 4: syntax error near unexpected token `c' line 4: `// (c) Copyright Rosetta Commons Member Institutions.'


Can any one help wiht this?



Wed, 2020-07-08 04:44
Andre Serobian