ConSurf. Can't open file *_protein_seq.fas

[GrimSmiler]

Problem:
when running

vagrant@debian-wheezy:/vagrant/ConSurf-develop$ consurf -PDB example/1lk2.pdb -CHAIN A -Out_Dir output_test/ -m --debug  -BlastFile output/_A.protein_query.blast --workdir workdir

error is displayed

ConSurf Version 1.0.6
====================================
Process Started at 10:32:6

Work dir: /vagrant/ConSurf-develop/workdir/ at /usr/local/bin/consurf line 181.
Output files could be found in output directory: output_test//
Debug log can be found in: /vagrant/ConSurf-develop/workdir//1lk2_A_ConSurf.log
Running mode is: _mode_pdb_no_msa (with ConSurf/ConSeq mode: CONSURF)
pdbParser=HASH(0x2885b68)
No msa mode - with PDB or without PDB MODE
/vagrant/muscle3.8.31 -in /vagrant/ConSurf-develop/workdir//PDB_SEQRES_1lk2_A.fasta2 -out /vagrant/ConSurf-develop/workdir//PDB_SEQRES_1lk2_A.aln -clwstrict -quiet at /usr/local/bin/consurf line 867.
Starting from predefined BLAST file: output/_A.protein_query.blast

prepareMSA::choose_homologoues_from_blast : can't open file /vagrant/ConSurf-develop/workdir//1lk2_A_protein_seq.fas for reading

Solution:
Find the sequence of the protein You are looking for (in this exmaple -> 1lk2 with Chain ID = A)

GPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQEGPEYWERETQKAKGNEQSFRVDLRT
LLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDGCDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYL
EGTCVEWLRRYLKNGNATLLRTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGT
FQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRW

and create a file in your folder you specified for --workdir
filename = pdbID_chainID_protein_seq.fas (1lk2_A_protein_seq.fas)
and the contents should be:

>PDB_SEQRES
GPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQEGPEYWERETQKAKGNEQSFRVDLRT
LLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDGCDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYL
EGTCVEWLRRYLKNGNATLLRTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGT
FQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRW

Now rerun ConSurf.