Scan one or more sequences with a simple frequency matrix

1

I am trying to get the image that gives haddock score vs. RMSD from best graph By using this command $HADDOCKTOOLS/ana_clusters.csh -best 4 analysis/cluster.out

However, I am getting the following error

Profile or weight matrix file: Error: Unable to open file ‘refe site_specific_120w.pdb’ for input
Profile or weight matrix file: Error: Unable to open file ‘mobi site_specific_88w.pdb’ for input
Died: profit terminated: Bad value for ‘-infile’ and no more retries
Scan one or more sequences with a simple frequency matrix
Profile or weight matrix file: Error: Unable to open file ‘refe site_specific_120w.pdb’ for input
Profile or weight matrix file: Error: Unable to open file ‘mobi site_specific_46w.pdb’ for input
Died: profit terminated: Bad value for ‘-infile’ and no more retries
Scan one or more sequences with a simple frequency matrix
Profile or weight matrix file: Error: Unable to open file ‘refe site_specific_120w.pdb’ for input
Profile or weight matrix file: Error: Unable to open file ‘mobi site_specific_113w.pdb’ for input
Died: profit terminated: Bad value for ‘-infile’ and no more retries
Scan one or more sequences with a simple frequency matrix
Profile or weight matrix file: Error: Unable to open file ‘refe site_specific_120w.pdb’ for input
Profile or weight matrix file: Error: Unable to open file ‘mobi site_specific_21w.pdb’ for input
Died: profit terminated: Bad value for ‘-infile’ and no more retries

2

Have you install the correct version of profit?

3

profit -h is giving me this ==>

Scan one or more sequences with a simple frequency matrix
Version: EMBOSS:6.6.0.0

** Standard (Mandatory) qualifiers:**
** [-infile] infile Profile or weight matrix file**
** [-sequence] seqall Sequence(s) filename and optional format, or**
** reference (input USA)**
** [-outfile] outfile [*.profit] Output file name**

** Additional (Optional) qualifiers: (none)**
** Advanced (Unprompted) qualifiers: (none)**
** General qualifiers:**
** -help boolean Report command line options and exit. More**
** information on associated and general**
** qualifiers can be found with -help -verbose**

4

This is not the profit software you need for HADDOCK :slight_smile:

http://www.bioinf.org.uk/software/profit/