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
Received on Fri May 18 2012 - 17:30:04 PDT
