Removing the dec_verbose variable from the mdin files did help with the
"error in reading namelist cntrl". Yet I did not quite understand it in
that AMBRE11/AT1.5 works fine with dec_verbose variable...
Qiong
On Sat, May 19, 2012 at 10:55 AM, Qiong Zhang <qiong.zhang.qzh.gmail.com>wrote:
> Hi Bill !
> Sorry, there is something new.
> When I removed the dec_verbose variable from the mdin files and rerun it
> with the -use-mdins, at the end of
> _MMPBSA_complex_gb.mdout.0 file, it got this error:
>
> " Unit 30 Error on OPEN: _MMPBSA_dummycomplex.inpcrd.1"
> The one you mentioned in a previous mail. So how shall I fix this problem
> please?
> Thanks!
> Qiong
>
>
>
> On Sat, May 19, 2012 at 9:55 AM, Bill Miller III <brmilleriii.gmail.com>wrote:
>
>> 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
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Sat May 19 2012 - 08:30:03 PDT
