Hi Bill,
After I remove the dec_verbose variable from the mdin files and rerun it
with the -use-mdins as you suggested, the "namelist cntrl error" is solved !
But at the end of _MMPBSA_complex_gb.mdout.0 file (see attached), it got
this error:
" Unit 30 Error on OPEN: _MMPBSA_dummycomplex.inpcrd.1"
Is it because _MMPBSA_dummycomplex.inpcrd.1 has not been produced? There
are only _MMPBSA_dummy*.inpcrd files. I tried to copy
_MMPBSA_dummycomplex.inpcrd to _MMPBSA_dummycomplex.inpcrd.1, and then
rerun it , but it did not work. _MMPBSA_dummycomplex.inpcrd.1 will be
removed.
Could you please suggest what I should do to solve this prolem? Great
thanks!
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
> > > > >
> > > > _______________________________________________
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> > > > 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 Mon May 21 2012 - 18:00:03 PDT
