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
Received on Fri May 18 2012 - 14:30:04 PDT
