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
>
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Received on Fri May 18 2012 - 15:00:03 PDT
