我需要一些帮助来运行这个代码。我从(http://easybioinfo.free.fr/?q=content/amber-trajectory-gromacs-xtc-conversion)中获取了此代码。 我正试着把琥珀轨道转换成格罗马克轨道。
当我执行这段代码时,我会得到一些错误。我在此代码下面粘贴错误:
#!/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$
有关信息,我正在使用Ubuntu11.10(64位)。
如何更正此错误?谢谢你的帮助。 谢谢您。
系统命令“ptraj”似乎无法生成“.pdb”文件。
我建议更改以下行,以免抑制可能的错误:
重新涂抹:
问题可能是,在Ubuntu11.x/bin/sh中链接到/bin/dash而不是bin bash。
检查链接:
如果/bin/sh是/bin/dash的链接,请将其更改为/bin/bash。
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