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AbinitioRelax with restraints/constraints

Submitted by jtmacd on Mon, 2011-07-11 07:07

Hi all,

Is it possible to do fragment assembly using AbinitioRelax with harmonic distance restraints.

I tried running it with this command line:

AbinitioRelax.linuxgccrelease -database ~/rosetta_database
-in:file:fasta t000_.fasta -in:file:native native.pdb
-in:file:frag3 aat000_03_05.200_v1_3
-in:file:frag9 aat000_09_05.200_v1_3
-abinitio:relax -relax:fast
-abinitio::increase_cycles 10 -abinitio::rg_reweight 0.5 -abinitio::rsd_wt_helix 0.5 -abinitio::rsd_wt_loop 0.5
-use_filters true
-psipred_ss2 t000_.psipred_ss2
-out:file:silent beta1_zn_preds.out

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Rosetta 3 - General

Error while compiling Rosetta 3.2. on Ubuntu 11.04 (AMD64)

Submitted by jkrellenstein on Wed, 2011-07-06 08:47

Hi,

I am trying to build Rosetta 3.2 on my ubuntu box through scon. After modifying the source in accordance with htt-DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.5 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/protocols/jd2/archive/ArchiveManager.cc
{standard input}: Assembler messages:
{standard input}:535948: Warning: end of file in string; '"' inserted
g++: Internal error: Killed (program cc1plus)
Please submit a full bug report.

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Rosetta 3 - Build/Install

error while loading shared libraries: libdevel.so

Submitted by jarek on Wed, 2011-07-06 03:11

I have successfully built rosetta 3.2.1 on fedora14, but
now whenever I try to execute any of the programs I get the following message:
error while loading shared libraries: libdevel.so: cannot open shared object file: No such file or directory

Do I need to set up some path variables? I haven't found any info in the manual.

Thanks for your help,

Jarek

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Rosetta 3 - Build/Install

How to define pi-pi stacking in cst file?

Submitted by lzx32 on Mon, 2011-07-04 23:47

Dear developers,

In the design of the kemp enzyme, a pseudoatom (X1) that represents the aromatic moeity was introduced to define the pi-pi stacking between an aromatic residue and the ligand. The block from the cst file is shown here:

#block 5 for aromatic binding

CST::BEGIN
TEMPLATE:: ATOM_MAP: 1 atom_name: X1 C10 C12
TEMPLATE:: ATOM_MAP: 1 residue3: D2N

TEMPLATE:: ATOM_MAP: 2 atom_type: aroC,
TEMPLATE:: ATOM_MAP: 2 residue1: WFY

CONSTRAINT:: distanceAB: 3.50 0.20 50.00 0
CONSTRAINT:: angle_A: 90.00 5.00 50.00 360.00

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Rosetta 3 - Applications

Compiling Rosetta 3.2 on Mac OS X using scons

Submitted by nkemjika on Thu, 2011-06-30 00:19

hi & thanks in advance,

preamble:

Mac OS X version: 10.6.8 | # Processors: 1
Rosetta version: 3.2
scons version: 2.1.0.alpha.20101125
Xcode version: 3.2.6
UNIX Shell: bash

problem:

i'm having difficulties compiling Rosetta with scons.
so far, i have followed the steps on the rosetta user guide page (at: (http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/)) to no avail.

first i installed scons without administrative privileges using the command:

$ python setup.py install --prefix=$HOME

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Rosetta 3 - Build/Install

rosetta 2.1.1- Installation problems in mac os x 10.6

Submitted by cctristan on Tue, 2011-06-28 11:33

Hi all, I have to install rosetta 2.1.1 since some code has been modified in this version by ourselves for special use two years ago. Now I have a problem about the installation.

I have successfully built rosetta 2.1.1 in Redhat by
$ make gcc64

the gcc version is :
gcc (GCC) 4.1.2 20070626 (Red Hat 4.1.2-14)
Copyright (C) 2006 Free Software Foundation, Inc.

However when I tried to build it in mac os x 10.6, I came across some errors.

In mac os x 10.6.8,

gcc version:
i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3)

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Rosetta++ - Build/Install

How to integrate Rosetta code to my program?

Submitted by Lsg on Tue, 2011-06-28 07:18

Hi.

I am a beginner with Rosetta, and was wondering if I can link its code (like any other library) to my program and use/call especial modules of it in my code. I can't decide it by reading the documentation on the website... Seems Rosetta isn't meant to be used in this way...

I'm specifically after the scoring functions (to calculate energies among atoms of a residue and also pairwise energies between each pair of residues). One option for me is to implement the terms of the energy function, and the other is using an existing library. Which one do you recommend?

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Rosetta 3 - General

secondary structure prediction for generation of fragment libraries

Submitted by xpzhang on Sat, 2011-06-25 00:47

I found that the "psipred" installed at three different places generated different results for one sequence (Rad59, please focus on the 40 aa at its N-terminus). Is that because their version? Which "psipred" is more reliable?

1. "Fragment Libraries" server (v2.6): http://robetta.bakerlab.org/downloads/fragments/22521/
2. the SYMPRED server (v ?): http://zeus.few.vu.nl/jobs/aeb9f401c184595c85e6ef7aaef6defe/
3. A local installed Psipred copy (v. 3.2 ?).

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Rosetta 3 - General

Floppytail modelling

Submitted by felipet on Fri, 2011-06-24 09:23

Hi,

sorry if this question is too basic, but I'm trying to use FloppyTail to model the C-terminus of a structure (the starting model was generated with robetta) and the run allways crashed.

when I run the test available (complex_readytail_final_nozn.pdb) the program works fine!

I tried many things with the pdb file, but I allways have the same problem

the options are basically the same as the test, obviusly changing the -flexible_start_resnum

the log:

Warning: no movable positions in ShearMover!
apps.public.scenarios.FloppyTail: 96 -169.666 -169.666

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Rosetta 3 - Applications

rosetta protein protein docking start up

Submitted by vk on Fri, 2011-06-24 09:01

Hi all

I just tried to install Rosetta 3.2.1 X64 bit in Redhat linux, guessing managed to install the software after initial trouble.
But do not know how to proceed to for doing docking and other usage of software. I did gone through the guide but not
clear enough for me.

Please how can I set up the environment and run either command mode or graphical interface of Rosetta for docking and other
calculations.

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