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flexpepdock flag "-packing:unboundrot"

I'm running flexpepdock with the flag "-unboundrot" and getting this error when I set the -nstruct flag manually (versus using the default of 1).

>[path to rosetta]/FlexPepDocking.linuxgccrelease
-database [path to db]
-s input.pdb
-native native.pdb
-receptor_chain 'A'
-peptide_chain 'H'
-rep_ramp_cycles 2
-mute protocols.jd2.JobDistributor
-nstruct 1

ERROR: No values of the appropriate type specified for multi-valued option -packing:unboundrot

Post Situation: 

rosetta 3.2.1 on mac os 10.6.8 - compiling problem

I am having trouble compiling rosetta. In the directory rosetta_source I ran varous "python mode=release [etc]" commands and ended up with various errors. Below I put three examples. I have installed the XCode tools and have gcc version 4.2. I don't want to install another version since seems to require other programs (gmp and mpfr) and I have run into problems compiling them.

>python mode=release bin -j2
src/apps/public/ sorry, unimplemented: 64-bit mode not compiled in

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AbinitioRelax with restraints/constraints

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


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/
{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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error while loading shared libraries:

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: 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,


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How to define pi-pi stacking in cst file?

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

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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Compiling Rosetta 3.2 on Mac OS X using scons

hi & thanks in advance,


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


i'm having difficulties compiling Rosetta with scons.
so far, i have followed the steps on the rosetta user guide page (at: ( to no avail.

first i installed scons without administrative privileges using the command:

$ python install --prefix=$HOME

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rosetta 2.1.1- Installation problems in mac os x 10.6

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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How to integrate Rosetta code to my program?


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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