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
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Received on Sat May 19 2012 - 07:00:03 PDT
