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-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 On May 20, 2012, at 1:01 AM, Qiong Zhang <qiong.zhang.qzh.gmail.com> wrote: > Removing the dec_verbose variable from the mdin files did help with the > "error in reading namelist cntrl". Yet I did not quite understand it in > that AMBRE11/AT1.5 works fine with dec_verbose variable... > Qiong > > > On Sat, May 19, 2012 at 10:55 AM, Qiong Zhang <qiong.zhang.qzh.gmail.com>wrote: > >> Hi Bill ! >> Sorry, there is something new. >> When I removed the dec_verbose variable from the mdin files and rerun it >> with the -use-mdins, at the end of >> _MMPBSA_complex_gb.mdout.0 file, it got this error: >> >> " Unit 30 Error on OPEN: _MMPBSA_dummycomplex.inpcrd.1" >> The one you mentioned in a previous mail. So how shall I fix this problem >> please? >> Thanks! >> Qiong >> >> >> >> On Sat, May 19, 2012 at 9:55 AM, Bill Miller III <brmilleriii.gmail.com>wrote: >> >>> Qiong, >>> >>> One more attempt. Can you remove the dec_verbose variable from the >>> _MMPBSA_gb_decomp_com.mdin, _MMPBSA_gb_decomp_rec.mdin, and >>> _MMPBSA_gb_decomp_lig.mdin files and then re-run MMPBSA.py with the >>> -use-mdins flag? This is the only potential problem that I can see with >>> the >>> cntrl namelist at the moment. And my theory is that this was added as a >>> variable in sander for Amber 12, but was not in Amber 11. And that's why >>> you are getting this error, but I was not. >>> >>> Let me know if that works or not. >>> >>> -Bill >>> >>> On Fri, May 18, 2012 at 11:00 PM, Qiong Zhang <qiong.zhang.qzh.gmail.com >>>> wrote: >>> >>>> Hi Bill, >>>> Thank you for the files. I did what you suggested. Unfortunately, with >>> your >>>> mdin files, I still got this sander problem saying "error in reading >>>> namelist cntrl". Not knowing why this happened... >>>> Many thanks for your help. :-) >>>> Regards, >>>> Qiong >>>> >>>> On Fri, May 18, 2012 at 8:20 PM, Bill Miller III <brmilleriii.gmail.com >>>>> wrote: >>>> >>>>> So according to your error message, sander is having a problem reading >>>> the >>>>> sander input file written by MMPBSA.py. Unfortunately, I can't see >>> where >>>>> the problem is. The input file being written by my version of >>> MMPBSA.py >>>> is >>>>> slightly different, but works fine for me. I have attached the actual >>>>> sander input files to this e-mail. Try using those by utilizing the >>>>> -use-mdins flag for MMPBSA.py. >>>>> >>>>> MMPBSA.py -i mmgbsa.in -cp 9nd-35w.top -rp 9nd.top -lp 35w.top -y >>>>> 9nd-35w.mdcrd -use-mdins >>>>> >>>>> Note that you also will not want to use the -O flag in the command >>> since >>>>> that will obviously remove those files before the calculation. You >>> will >>>>> also need to switch which prmtop corresponds to the receptor and >>> ligand >>>>> from how you had it compared to how I used it. Good luck and I hope >>> this >>>>> works for you. >>>>> >>>>> -Billy >>>>> >>>>> On Fri, May 18, 2012 at 5:37 PM, Qiong Zhang < >>> qiong.zhang.qzh.gmail.com >>>>>> wrote: >>>>> >>>>>> Here it is. >>>>>> In my case, the calculation of complex contribution is not >>> finished... >>>>>> Qiong >>>>>> >>>>>> On Fri, May 18, 2012 at 5:06 PM, Bill Miller III < >>>> brmilleriii.gmail.com >>>>>>> wrote: >>>>>> >>>>>>> I did see the CalcError message. It following the message that I >>>>>> previously >>>>>>> showed about the _MMPBSA_dummycomplex.inpcrd.1 missing file. >>>>>>> >>>>>>> Beginning GB calculations with >>>>>>> /Users/bmiller/Source/Amber_git_HPC/amber/bin/sander >>>>>>> calculating complex contribution... >>>>>>> calculating receptor contribution... >>>>>>> >>>>>>> Error opening unit 30: File "_MMPBSA_dummyreceptor.inpcrd.1" is >>>>>> missing >>>>>>> or unreadable >>>>>>> CalcError: /Users/bmiller/Source/Amber_git_HPC/amber/bin/sander >>>> failed >>>>>> with >>>>>>> prmtop 9nd.top! >>>>>>> Exiting. All files have been retained. >>>>>>> >>>>>>> Can you attach your entire _MMPBSA_complex_gb.mdout.0 file in an >>>>> e-mail? >>>>>>> >>>>>>> -Bill >>>>>>> >>>>>>> On Fri, May 18, 2012 at 3:57 PM, Qiong Zhang < >>>>> qiong.zhang.qzh.gmail.com >>>>>>>> wrote: >>>>>>> >>>>>>>> I got this file _MMPBSA_dummyreceptor.inpcrd produced and the >>>> program >>>>>>>> stopped during the calculation of complex contribution >>>>>>>> (_MMPBSA_complex_gb.mdout.0). >>>>>>>> >>>>>>>> Qiong >>>>>>>> >>>>>>>> On Fri, May 18, 2012 at 3:52 PM, Qiong Zhang < >>>>>> qiong.zhang.qzh.gmail.com >>>>>>>>> wrote: >>>>>>>> >>>>>>>>> I did not see this error - Error opening unit 30: File >>>>>>>>> "_MMPBSA_dummyreceptor.inpcrd.1" is missing or unreadable. >>>>>>>>> But did you see sander error I mentioned above please? >>>>>>>>> Qiong >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, May 18, 2012 at 3:46 PM, Bill Miller III < >>>>>>> brmilleriii.gmail.com >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> I ran the calculation and got the following error message >>>> written >>>>> to >>>>>>> the >>>>>>>>>> screen: >>>>>>>>>> >>>>>>>>>> Error opening unit 30: File >>> "_MMPBSA_dummyreceptor.inpcrd.1" >>>> is >>>>>>>> missing >>>>>>>>>> or unreadable >>>>>>>>>> >>>>>>>>>> Did you see something like this, also? Something similar was >>>> also >>>>> at >>>>>>> the >>>>>>>>>> end of the mdout file. >>>>>>>>>> >>>>>>>>>> Once I fixed this bug the calculation ran just fine for me. >>> Let >>>> me >>>>>>> know >>>>>>>> if >>>>>>>>>> this is actually your problem and I will let you know how to >>> fix >>>>> it. >>>>>>>>>> >>>>>>>>>> -Bill >>>>>>>>>> >>>>>>>>>> On Fri, May 18, 2012 at 3:14 PM, Qiong Zhang < >>>>>>> qiong.zhang.qzh.gmail.com >>>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> The files have been sent to you. Thanks! >>>>>>>>>>> Qiong >>>>>>>>>>> >>>>>>>>>>> On Fri, May 18, 2012 at 3:02 PM, Bill Miller III < >>>>>>>> brmilleriii.gmail.com >>>>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>>> Can you send me the files (prmtops, 1-2 frame trajectory, >>>> and >>>>>> your >>>>>>>>>> input >>>>>>>>>>>> file) and I will try them and see if I can reproduce the >>>>> error? >>>>>>>>>>>> >>>>>>>>>>>> -Bill >>>>>>>>>>>> >>>>>>>>>>>> On Fri, May 18, 2012 at 2:56 PM, Qiong Zhang < >>>>>>>>>> qiong.zhang.qzh.gmail.com >>>>>>>>>>>>> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Thanks for the suggestion. But you are right. Tried >>>> setting >>>>>>>>>>> use_sander=1, >>>>>>>>>>>>> the same problem still appeared. >>>>>>>>>>>>> Qiong >>>>>>>>>>>>> >>>>>>>>>>>>> On Fri, May 18, 2012 at 2:49 PM, Bill Miller III < >>>>>>>>>>> brmilleriii.gmail.com >>>>>>>>>>>>>> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Try setting use_sander=1 in your MMPBSA.py input >>> file. >>>> The >>>>>>>>>>>> decomposition >>>>>>>>>>>>>> analysis can only be run with the sander executable >>>> (e.g. >>>>> it >>>>>>>>>> cannot >>>>>>>>>>> be >>>>>>>>>>>>> done >>>>>>>>>>>>>> with mmpbsa_py_energy). By setting use_sander=0 in >>> your >>>>>> input >>>>>>>>>> file, >>>>>>>>>>> you >>>>>>>>>>>>> may >>>>>>>>>>>>>> be trying to get MMPBSA.py to use mmpbsa_py_energy >>> for >>>> the >>>>>>>> energy >>>>>>>>>>>>>> calculations instead of using sander like it should. >>>>>>>>>>>>>> >>>>>>>>>>>>>> I am not convinced this is the issue since sander is >>>>>> mentioned >>>>>>>> in >>>>>>>>>> the >>>>>>>>>>>>>> output message, but either way your input file is >>>>>>> contradicting >>>>>>>>>> what >>>>>>>>>>>> the >>>>>>>>>>>>>> program should be doing with a decomposition >>> calculation >>>>>>> anyway. >>>>>>>>>>>>>> >>>>>>>>>>>>>> -Bill >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Fri, May 18, 2012 at 2:43 PM, Qiong Zhang < >>>>>>>>>>>> qiong.zhang.qzh.gmail.com >>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> In fact, in the command line I used >>>>>>> $AMBERHOME/bin/MMPBSA.py, >>>>>>>>>> so it >>>>>>>>>>>>> won't >>>>>>>>>>>>>>> go wrong. And in the output it clearly shows the >>>>> MMPBSA.py >>>>>>>>>>>> executables >>>>>>>>>>>>>>> (mmpbsa_py_energy,cpptraj) are from AT12. And >>> sander >>>> is >>>>>> from >>>>>>>>>>> Amber11. >>>>>>>>>>>>>>> What else should I check please? Thanks! >>>>>>>>>>>>>>> Qiong >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Fri, May 18, 2012 at 2:35 PM, Bill Miller III < >>>>>>>>>>>>> brmilleriii.gmail.com >>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> If you type `which MMPBSA.py` does the MMPBSA.py >>>>>>> executable >>>>>>>>>> from >>>>>>>>>>>>>>>> AmberTools12 appear correctly? And have you >>> applied >>>>> all >>>>>>>>>> bugfixes >>>>>>>>>>>> for >>>>>>>>>>>>>>>> AmberTools12? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> -Bill >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Fri, May 18, 2012 at 2:29 PM, Qiong Zhang < >>>>>>>>>>>>>> qiong.zhang.qzh.gmail.com >>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Dear Amber users, >>>>>>>>>>>>>>>>> I compiled the newest Ambertools12 under my >>> home >>>>>>>> directory. >>>>>>>>>>> And I >>>>>>>>>>>>>> need >>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>> use Amber11 in another directory in the >>> cluster. >>>> In >>>>>>> order >>>>>>>> to >>>>>>>>>>> use >>>>>>>>>>>>> the >>>>>>>>>>>>>>>> Amber >>>>>>>>>>>>>>>>> executables from amber11/bin, but to use the >>>>>> AmberTools >>>>>>> 12 >>>>>>>>>>>>>> executables >>>>>>>>>>>>>>>> from >>>>>>>>>>>>>>>>> amber12/bin, I followed the instructions by >>> Jason >>>> on >>>>>>> this >>>>>>>>>> page >>>>>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>> >>>> http://jswails.wikidot.com/installing-ambertools-12-and-older-amber >>>>>>>>>>>>>>>>> export AMBERHOME=/home/user/amber12 >>>>>>>>>>>>>>>>> export >>>>>>>>>> PATH=$PATH:/home/user/amber12/bin:/home/user/amber11/bin >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> The input file is as follows: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> &general >>>>>>>>>>>>>>>>> search_path=1,startframe=1, endframe=1, >>>> interval=1, >>>>>>>>>> verbose=2, >>>>>>>>>>>>>>>>> strip_mask=":Cl-", entropy=0, use_sander=0, >>>>>>>>>>>>>> netcdf=0,debug_printlevel=1 >>>>>>>>>>>>>>>>> / >>>>>>>>>>>>>>>>> &gb >>>>>>>>>>>>>>>>> igb=2 >>>>>>>>>>>>>>>>> / >>>>>>>>>>>>>>>>> &decomp >>>>>>>>>>>>>>>>> idecomp=1, print_res="1-2",dec_verbose=2 >>>>>>>>>>>>>>>>> / >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> With search_path=1, the program did find the >>>> sander, >>>>>> but >>>>>>>>>> ended >>>>>>>>>>>>> with a >>>>>>>>>>>>>>>>> sander error: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> *CalcError: /lap/amber/11.0.17_AT1.5/bin/sander >>>>> failed >>>>>>>> with >>>>>>>>>>>> prmtop >>>>>>>>>>>>>>>>> ../prmtop2/9nd-35w.top* >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> And at the end of file >>> _MMPBSA_complex_gb.mdout.0, >>>>> it >>>>>>> has: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Here is the input file: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> File generated by MMPBSA.py >>>>>>>>>>>>>>>>> &cntrl >>>>>>>>>>>>>>>>> ncyc=0, cut=999.0, nsnb=99999, gbsa=2, >>>>>>>>>>>>>>>>> ntb=0, dec_verbose=2, imin=5, >>>>>>>>>>>>>>>>> idecomp=1, extdiel=80.0, igb=2, >>>>>>>>>>>>>>>>> surften=0.0072, >>>>>>>>>>>>>>>>> / >>>>>>>>>>>>>>>>> Residues considered as REC >>>>>>>>>>>>>>>>> RRES 2 36 >>>>>>>>>>>>>>>>> END >>>>>>>>>>>>>>>>> Residues considered as LIG >>>>>>>>>>>>>>>>> LRES 1 1 >>>>>>>>>>>>>>>>> END >>>>>>>>>>>>>>>>> Residues to print >>>>>>>>>>>>>>>>> RES 1 2 >>>>>>>>>>>>>>>>> END >>>>>>>>>>>>>>>>> END >>>>>>>>>>>>>>>>> * error in reading namelist cntrl* >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> If I commented out the decomp part in the input >>>>> file, >>>>>> it >>>>>>>>>> works >>>>>>>>>>>>> fine. >>>>>>>>>>>>>>> And >>>>>>>>>>>>>>>>> there is no problem if Amber11 and >>> Ambertools1.5 >>>>> under >>>>>>> the >>>>>>>>>> same >>>>>>>>>>>>>>> directory >>>>>>>>>>>>>>>>> were used. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Could you please suggest what might be wrong >>> here? >>>>>>> Thanks! >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Qiong >>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>> 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/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/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/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/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/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/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/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sun May 20 2012 - 19:00:03 PDT