我需要帮助运行这段代码。我从（http://easybioinfo.free.fr/?q=content/amber-trajectory-gromacs-xtc-conversion）获得了这段代码。
当我执行这段代码时，出现了一些错误。我将这些错误粘贴在以下代码下方：
#!/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_\"$0\".pdb\" }' | sh ; cd ../")
pdb_files=fnmatch.filter(os.listdir("pdb_tmp"),"*.pdb")
pdb_files.sort(key=ALPHANUM_KEY) #sort by these numbers in filenames
if csn==1:
os.system("editconf -f pdb_tmp/mdcrd_1.pdb -o "+outputPref+"_t1_top.gro >/dev/null 2>&1")
for pdb in pdb_files:
os.system("echo \"0\" | trjconv -s pdb_tmp/"+pdb+" -f pdb_tmp/"+pdb+" -o xtc_tmp/traj_"+str(csn)+".pdb.xtc -t0 "+str(csn)+" >/dev/null 2>&1")
csn+=1
if os.path.exists(outputPref+"_traj.xtc"):
os.system("trjcat -f "+outputPref+"_traj.xtc xtc_tmp/*.pdb.xtc -o "+outputPref+"_traj.xtc >& trajcat.log")
else :
os.system("trjcat -f xtc_tmp/*.pdb.xtc -o "+outputPref+"_traj.xtc >& trajcat.log")
os.system("rm -rf pdb_tmp/*.pdb")
os.system("rm -rf xtc_tmp/*.xtc")
os.remove("ptraj_tmp.ptr")
os.system("rmdir pdb_tmp")
os.system("rmdir xtc_tmp")
错误如下：
vijay@glycosim:~/Simulation-Folder-Feb2013/chapter5-thermo-paper2-Vj/analysis-malto-/28-difusion-coeff-malto-thermo/convert-gromacs-format$ 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$
提供信息，我正在使用Ubuntu 11.10（64位）。
如何纠正这个错误？感谢任何帮助。谢谢。