PEPSPEC

[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

[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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