sh: Syntax error: Bad fd number [closed]

问题:

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.

回答1:

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 

回答2:

It seems that the system command "ptraj" fails to generate that ".pdb" file/files.

I would suggest to change the following line in order to not suppress possible errors:

os.system("ptraj "+top +" ptraj_tmp.ptr >/dev/null 2>&1") 

repace with:

os.system("ptraj "+top +" ptraj_tmp.ptr") 

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