Unsolved

Hi all,

Was just wondering, are there any options I can use to force Rosetta to ignore PDB defined hydrogens and rebuild all hydrogens (including non-polar) when loading into the score, relax, rosetta_scripts Apps? I particularly need to rebuild backbone non-polar hydrogens as these are bad in the input PDB files but Rosetta generally seems to leave these untouched.

I have tried the options:

-no_optH false
and
-skip_hydrogens true

Dear Sir,
Hello!. I am Irshad Baig, pursuing PhD in Biochemistry.

I am writing you to seek your help regarding 3D structure prediction of ss DNA and ssDNA-Protein docking studies.

Infact, I am trying to build 3D model structure for my ss DNA aptamer, as i am further interested to study DNA -protein interaction through docking. However, I did not succeed in building 3D struture for ss DNA aptamer.

I am trying to use python script under linux in which I import rosetta module('from rosetta import *) and use rosetta methods. But I got this error. What is the reason for that and does anyone know how to fix it?

ERROR: Unable to open weights/patch file. None of (./)standard or (./)standard.wts or /usr/local/share/PyRosetta/rosetta_database/scoring/weights/standard or /usr/local/share/PyRosetta/rosetta_database/scoring/weights/standard.wts exist
ERROR:: Exit from: src/core/scoring/ScoreFunction.cc line: 2967
Traceback (most recent call last):

We can make fragment libraries from Free Web Server : Robetta Server or Rosetta.And I want to know more details about how to create the fragment libraries.I searched in the Rosetta user Guide,just found the paper(Gront D, Kulp DW, Vernon RM, Strauss CEM and Baker D, "Generalized fragment picking in Rosetta: design, protocols and applications", submitted to PLoS ONE)。Is there any paper about how to create the fragment libraries except that?