Scoring

Hi,

I'm new to Rosetta and currently working through the tutorials.

I often recognized that  the the score values produced by the recent version "Rosetta 2019.47" on my computer differ from the ones cited in the tutorials and given expected_output.

e.g.:

in the Scoring Tutorial  (subchapter "Changing the Score Function") the command

ROSETTA3/bin/score_jd2.linuxgccrelease @flag_docking

with flags

Hi all,

I am trying to calculate Ddg for a protein complex, which is made of 3 chains: A, B and C.

The chains B and C have a zinc-finger each, which are a zinc ion complexed by four CYS side-chains.

To calculate the Ddg I am using the SetupPoissonBoltzmannPotential mover followed by the Ddg filter, in order to separate chain B from chain A+C and calculate the binding energy.

Hello, I am trying the score app in the tutorials and meet an fatal error.

I work on CentOS 7 and my rosetta version is rosetta_src_2019.40.60963_bundle.

At first, I just used the command given by the instruction, it is:

score.mpi.linuxgccrelease -in:file:s input_files/1qys.pdb -in:file:native input_files/from_rcsb/1qys.pdb -ignore_waters

however, it stoped after a few seconds and the last lines of log is:

Hey Guys,

We are trying to use  "InterfaceAnalyzer"  to  analyze a  PDB,  then we get this:

......

.....

core.conformation.Conformation: [ WARNING ] missing heavyatom: C7 on residue pdb_HSD 152
core.conformation.Conformation: [ WARNING ] missing heavyatom: O4 on residue pdb_HSD 152
Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job 'complex_0_0001'
Error: [ ERROR ]