sh: Syntax error: Bad fd number
Question: I need some help in running this code. I took this code from
(<http://easybioinfo.free.fr/?q=content/amber-trajectory-gromacs-xtc-
conversion>). I am trying to convert amber trajectory to gromacs trajectory.

When I execute this code, I get some errors. I paste the errors below this
code:

    
    
        #!/usr/bin/python
    
    #Workflow based on Trajectory Converter - v1.5 by: Justin Lemkul 
    #completely reimplemented and improved by Peter Schmidtke & Jesus Seco
    
    import sys,os,re,fnmatch
    
    if len(sys.argv)>4 :
        f=sys.argv[1]
        if not os.path.exists(f):
            sys.exit(" ERROR : Something you provided does not exist. Breaking up.\n\nUSAGE : python trajconv_peter.py  amberCrd amberTop trajDir trajPattern outPutPrefix\n\n \
    Example : python amber2xtc.py mdcrd.crd mdcrd.top md *.x.gz md_gromacs\n")
    else :
        sys.exit(" \n  USAGE : python amber2xtc.py AMBERCRD AMBERTOP TRAJDIR TRAJPATTERN OUTPUTPREFIX\n\
        Example : python amber2xtc.py mdcrd.crd mdcrd.top md *.x.gz md_gromacs\n\
        Note that the AmberCrd can also be a PDB file.\n")
    
    crd=sys.argv[1]
    top=sys.argv[2]
    trajdir=sys.argv[3]
    pattern=sys.argv[4]
    outputPref=sys.argv[5]
    
    traj_files=fnmatch.filter(os.listdir(trajdir),pattern) #get the fpocket output folders
    
    
    RE_DIGIT = re.compile(r'(\d+)')     #set a pattern to find digits
    ALPHANUM_KEY = lambda s: [int(g) if g.isdigit() else g for g in RE_DIGIT.split(s)]      #create on the fly function (lambda)    to return numbers in filename strings
    traj_files.sort(key=ALPHANUM_KEY)      #sort by these numbers in filenames
    
    print "Will convert the following files : "
    print traj_files
    
    csn=1
    for file in traj_files :
        ptrajtmp=open("ptraj_tmp.ptr","w")
        print "currently converting "+file
        ptrajtmp.write("trajin "+trajdir+os.sep+file+"\n")
        ptrajtmp.write("reference "+crd+"\n")
        ptrajtmp.write("center ~:WAT,CIO mass origin\n")
        ptrajtmp.write("image origin center :* byres familiar\n")
    
        ptrajtmp.write("trajout pdb_tmp/mdcrd.pdb pdb")
        ptrajtmp.close()
        if not os.path.exists("pdb_tmp"):
            os.mkdir("pdb_tmp")
    
        os.system("ptraj "+top +" ptraj_tmp.ptr >/dev/null 2>&1")
        if not os.path.exists("xtc_tmp"):
            os.mkdir("xtc_tmp")
        #move to *.pdb
        os.system("cd pdb_tmp; ls *.pdb.* | cut -f3 -d\".\" | awk '{print \"mv mdcrd.pdb.\"$0\" mdcrd_\"$0\".pdb\" }' | sh ; cd ../")   
        pdb_files=fnmatch.filter(os.listdir("pdb_tmp"),"*.pdb")
        pdb_files.sort(key=ALPHANUM_KEY)      #sort by these numbers in filenames   
        if csn==1:
            os.system("editconf -f pdb_tmp/mdcrd_1.pdb -o "+outputPref+"_t1_top.gro >/dev/null 2>&1")
    
        for pdb in pdb_files:
            os.system("echo \"0\" | trjconv -s pdb_tmp/"+pdb+" -f pdb_tmp/"+pdb+" -o xtc_tmp/traj_"+str(csn)+".pdb.xtc -t0 "+str(csn)+" >/dev/null 2>&1")
            csn+=1
        if os.path.exists(outputPref+"_traj.xtc"):
            os.system("trjcat -f "+outputPref+"_traj.xtc xtc_tmp/*.pdb.xtc -o "+outputPref+"_traj.xtc >& trajcat.log")
        else :
            os.system("trjcat -f xtc_tmp/*.pdb.xtc -o "+outputPref+"_traj.xtc >& trajcat.log")
        os.system("rm -rf pdb_tmp/*.pdb")
    
        os.system("rm -rf xtc_tmp/*.xtc")
    
    
    os.remove("ptraj_tmp.ptr")
    os.system("rmdir pdb_tmp")
    os.system("rmdir xtc_tmp")
    

The error is as below:

    
    
     vijay@glycosim:~/Simulation-Folder-Feb2013/chapter5-thermo-paper2-Vj/analysis-malto-/28-difusion-coeff-malto-thermo/convert-gromacs-format$ python2.7 amber2xtc.py malto-THERMO.crd malto-THERMO.top TRAJDIR malto*.traj md_gromacss
     Will convert the following files : 
     ['malto-thermo.set11.traj', 'malto-thermo.set12.traj', 'malto-thermo.set13.traj', 'malto-thermo.set14.traj', 'malto-thermo.set15.traj']
     currently converting malto-thermo.set11.traj
     ls: cannot access *.pdb.*: No such file or directory
     sh: Syntax error: Bad fd number
     currently converting malto-thermo.set12.traj
     ls: cannot access *.pdb.*: No such file or directory
     sh: Syntax error: Bad fd number
     currently converting malto-thermo.set13.traj
     ls: cannot access *.pdb.*: No such file or directory
     sh: Syntax error: Bad fd number
     currently converting malto-thermo.set14.traj
     ls: cannot access *.pdb.*: No such file or directory
     sh: Syntax error: Bad fd number
     currently converting malto-thermo.set15.traj
     ls: cannot access *.pdb.*: No such file or directory
     sh: Syntax error: Bad fd number
     vijay@glycosim:~/Simulation-Folder-Feb2013/chapter5-thermo-paper2-Vj/analysis-malto-/28-difusion-coeff-malto-thermo/convert-gromacs-format$
    

For information, I am using Ubuntu 11.10 (64 bit).

How this error can be corrected? Appreciate any help. Thank you.


Answer: The problem could be, that in Ubuntu 11.x /bin/sh is linked to /bin/dash and
not to bin bash.

check the link:

    
    
    ls -l /bin/sh
    

If /bin/sh is a link to /bin/dash, change it to /bin/bash.

    
    
    sudo mv /bin/sh /bin/sh.orig
    sudo ln -s /bin/bash /bin/sh
    

