Solved

Hi there,

I have a pdb file from CHARMM format. When I use

fixbb.default.linuxgccrelease -in:file:s step1_pdbreader.pdb -in:file:fullatom -resfile resfile_2 -ex1 -ex2 -extrachi_cutoff 1 -nstruct 50 >out

I got this:

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms:    1 A TRP TRP:NtermProteinFull:triazolamerC
core.io.pose_from_sfr.PoseFromSFRBuilder: missing:  CT1

and it skipped the first residue TRP.

Hello everyone,

I am trying to relax a structure while also applying constraints on spesific locations in order to force these locations to be a spesific distance appart.

so far my code is as follows:

Hi everyone,

I had to reinstall newest rosetta (rosetta_bin_linux_2017.39.59729_bundle), but after successful installation and compilation, when I want to get docking using following commands and script:; 

 ~/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/source/bin/rosetta_scripts.default.linuxgccrelease -database ~/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/database/ -nstruct 200 -s 1czH_1czW.pdb -ex1 -ex2 -parser:protocol  docking_stubs.xml

I'm trying to run abinitio to predict the structure of a mutant protein homologue. using thwe following command line options:

 AbinitioRelax.macosclangrelease  -in:file:native ./input_files/input.pdb -in:file:fasta ./input_files/ACSM3.txt -in:file:frag3 ./input_files/aat000_03_05.200_v1_3 -in:file:frag9 ./input_files/aat000_09_05.200_v1_3 -database $ROSETTA3_DB -nstruct 1 -out:path ./output_files/ -out:pdb -abinitio::increase_cycles 10 -abinitio:rg_reweight 0.5 -abinitio:rsd_wt_helix 0.5 -abinitio:rsd_wt_loop 0.5