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-- Best wishes, Qinghua Liao Ph.D student of Tianjin University, China At 2011-04-08，"Bill Miller III" <brmilleriii.gmail.com> wrote: >What version of AmberTools are you using? The installation is failing when >trying to compile the entropy code, which is a nab program. You will need to >be using the nab from AmberTools 1.4 or later in order for this to compile >correctly. AmberTools 1.4 opens into an amber11 directory tree, and since >the nab that is being used to compile here is in an amber10 directory >(/vol5/home/cadd/amber/amber10/bin/nab), then I am going to guess this is >your problem. You will either need to download and install AmberTools 1.4 >from the Amber website, or if you have already done that, make sure that >your environment is setup so that the the AmberTools 1.4 is used instead of >nab from Amber10. > >Good luck! > >-Bill > >On Fri, Apr 8, 2011 at 4:38 AM, fancy2012 <fancy2012.yeah.net> wrote: > >> Dear amber users, >> >> I meet a problem when I install MMPBSA.py on my computer. Here are the >> process of installation and errors: >> >> Before I compile it, I apply the patches first. But I guess that the >> patching is failed, just as showed like this: >> patching file src/mmpbsa_py/MMPBSA.py >> patching file src/mmpbsa_py/MMPBSA.py.MPI >> patching file src/mmpbsa_py/mmpbsa_entropy.nab >> patching file src/mmpbsa_py/Makefile >> Reversed (or previously applied) patch detected! Skipping patch. >> 1 out of 1 hunk ignored -- saving rejects to file >> src/mmpbsa_py/Makefile.rej >> patching file src/mmpbsa_py/utils.py >> patching file src/mmpbsa_py/MMPBSA.py.MPI >> Hunk #1 succeeded at 1020 (offset -3 lines). >> patching file src/mmpbsa_py/utils.py >> Hunk #1 FAILED at 4. >> 1 out of 4 hunks FAILED -- saving rejects to file >> src/mmpbsa_py/utils.py.rej >> >> >> So when I ran make serial in mmpbsa_py, it failed. Here are the errors: >> >> /bin/bash setup.sh >> Python version 2 detected. No file conversion necessary. >> /bin/cp MMPBSA.py *pyc /vol5/home/cadd/amber/amber10/bin >> /vol5/home/cadd/amber/amber10/bin/nab -o mmpbsa_py_nabnmode >> mmpbsa_entropy.nab >> mmpbsa_entropy.nab:58 fld 'ls_method' not in struct 'xo' >> mmpbsa_entropy.nab:58 operator '=': left operand has wrong class. >> mmpbsa_entropy.nab:58 unknown attribute 'ls_method' >> mmpbsa_entropy.nab:59 fld 'ls_maxiter' not in struct 'xo' >> mmpbsa_entropy.nab:59 operator '=': left operand has wrong class. >> mmpbsa_entropy.nab:59 unknown attribute 'ls_maxiter' >> mmpbsa_entropy.nab:60 fld 'ls_maxatmov' not in struct 'xo' >> mmpbsa_entropy.nab:60 operator '=': left operand has wrong class. >> mmpbsa_entropy.nab:60 unknown attribute 'ls_maxatmov' >> nab2c failed! >> make: [install] Error 1 (ignored) >> /bin/mv mmpbsa_py_nabnmode /vol5/home/cadd/amber/amber10/bin >> /bin/mv: cannot stat `mmpbsa_py_nabnmode': No such file or directory >> make: [install] Error 1 (ignored) >> >> >> >From the above lines, I guess it is the problem of patching, so could >> someone tell me how to figure it out? Any response will be highly >> appreciated. Thanks! >> -- >> Best wishes, >> >> Qinghua >> >> Ph.D student of Tianjin University, China >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > > > >-- >Bill Miller III >Quantum Theory Project, >University of Florida >Ph.D. Graduate Student >352-392-6715 >_______________________________________________ >AMBER mailing list >AMBER.ambermd.org >http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sun Apr 10 2011 - 03:30:03 PDT