Hi
when I analyze the results from the results zip file ( antibody-antigen.tgz) I encounter this error:
profit:: Too many arguments.
profit:: Too many arguments.
profit:: Too many arguments.
if: Expression Syntax.
when doing this command:
$HADDOCKTOOLS/ana_clusters.csh -best 4 analysis/cluster.out
But I did download profit and I am also able to see the rmsd column in the structures_haddock-sorted.stat
Do you know why?
Thank you
also when I am analyzing my results and I do
$HADDOCKTOOLS/ana_clusters.csh -best 4 analysis/cluster.out
The file clusters_haddock-sorted.stats_best4 is not created, the files file.list* are empty and also prints this error: Missing }.
and when I do $HADDOCKTOOLS/ana_structures.csh I have this error if: Expression Syntax. and also the file structures_haddock-sorted.stat is not created
could it be I have a problem with profit? how can I tell?
Thank you
Seems like a shell issue.
These are csh/tcsh scripts. Do you have csh/tcsh installed on your system?
Also before running those scripts you do have to source the haddock_configure script.
I usually use tcsh (and the code is csh)
And I did configure haddock before. Can it be something else?
Does this analysis work when you are running the examples?
@Miriam could you please show the full output of the following command?
$ csh $HADDOCKTOOLS/ana_clusters.csh -best 4 analysis/cluster.out
with this cammomd
(it make a lot of the files but not clusters_haddock-sorted.stats_best4)
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profit:: Too many arguments.
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profit:: Too many arguments.
profit:: Too many arguments.
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profit:: Too many arguments.
profit:: Too many arguments.
profit:: Too many arguments.
profit:: Too many arguments.
profit:: Too many arguments.
profit:: Too many arguments.
profit:: Too many arguments.
profit:: Too many arguments.
profit:: Too many arguments.
profit:: Too many arguments.
profit:: Too many arguments.
profit:: Too many arguments.
profit:: Too many arguments.
profit:: Too many arguments.
profit:: Too many arguments.
profit:: Too many arguments.
profit:: Too many arguments.
if: Expression Syntax.
and with this one cammond csh $HADDOCKTOOLS/ana_structures.csh
if: Expression Syntax.
Thank you!
sorry first section pasted twice
Thanks for posting the output, not very informative I’m afraid 
Did you get this antibody-antigen.tgz from one of the pre-calculated data in our website? If so could you please share the url?
yes
This, my results and protein-peptide results did not work
https://surfdrive.surf.nl/files/index.php/s/sf2FUVau1Iasocd
Thanks for sharing the files, with the archive you provided i’ve managed to run it without problems or any messages
$ cd antibody-antigen/antibody-antigen-run-2xl/structures/it1/water
$ $HADDOCKTOOLS/ana_clusters.csh -best 4 analysis/cluster.out
$ head -n 1 structures_haddock-sorted.stat it1/water UU114601
#struc haddock-score rmsd_all Einter Enb Evdw+0.1Eelec Evdw Eelec Eair Ecdih Ecoup Esani Evean Edani #NOEviol #Dihedviol #Jviol #Saniviol #veanviol #Daniviol bsa dH Edesolv
$ head -n 1 clusters_haddock-sorted.stat_best4 it1/water UU114601
#Cluster haddock-score sd rmsd sd rmsd-Emin sd Nstruc Einter sd Enb sd Evdw+0.1Eelec sd Evdw sd Eelec sd Eair sd Ecdih sd Ecoup sd Esani sd Evean sd Edani sd #AIRviol sd #dihedviol sd #Coupviol sd #Saniviol sd #Veanviol sd #Daniviol sd BSA sd #dH sd #Edesolv sd
So it seems like the issue related to your setup… I tested it on WSL with a vanilla CSH:
$ dpkg -l csh
Desired=Unknown/Install/Remove/Purge/Hold
| Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name Version Architecture Description
+++-==============-============-============-=================================
ii csh 20110502-7 amd64 Shell with C-like syntax
and in CentOS7 with tcsh
$ csh --version
tcsh 6.18.01 (Astron) 2012-02-14 (x86_64-unknown-linux) options wide,nls,dl,al,kan,sm,rh,color,filec
$ cat /etc/*-release | head -n 1
CentOS Linux release 7.9.2009 (Core)
This is a legacy c-shell script and i’m afraid there is not much I can still help you with 
Maybe one last suggestion would be to remove profit from the $PATH and try running the script without it.
I’ve done some search and this :: Too many arguments. seems to be related to CSH versions - if possible, try in a different computer.