I am using 2 proteins from the DBD5 which I have run through the simple interface on the haddock server which finishes a complete analysis.
On my local copy of haddock using the exact same protein files and residues, haddock errors with the following:
Error in the topology generation: prot_psf_A could not be created
I have run pdb_format.py on the files from the git repository and both seem fine and there is nothing I can determine from the generate_A/B.out files. They end like this:
ASSFIL: file ligand.pep opened.
CHAIN> coordinates @@$coor_infile
%ASSFIL-ERR: error opening file .//data/sequence/protein1.pdb
%ASSFIL error encountered: Error accessing file
(CNS is in mode: SET ABORT=NORMal END)
ABORT mode will terminate program execution.
Program will stop immediately.
…
On a side note, there seems to be 2 run.cns parameters required for a local haddock run which are not in the run.cns downloaded from a serverrun, specifically:
{===>} clust_meth=“FCC”;
{===>} clust_cutoff=0.75;