# PEPSPEC

2 posts / 0 new
PEPSPEC
#1

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

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

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 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?

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