Dear Jason,
Thanks for your response. We are currently busy on the other project.
We will try the solutions you kindly mention and let you know in the
following weeks.
Many thanks,
Henry
On Tue, Feb 12, 2013 at 7:01 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Tue, Feb 12, 2013 at 1:23 AM, <psu4.uic.edu> wrote:
>
> > Dear Amber,
> >
> > Amber 12 was built with Intel/11.1.
> >
> > In the _MMPBSA_gb.mdin, it says:
>
>
> > Error opening unit 30: File "_MMPBSA_dummycomplex.inpcrd" is missing
> or
> > unreadable
> >
>
> This looks like the error that was fixed by bugfix.8 in AmberTools 12. But
> you say you saw this in _MMPBSA_gb.mdin? That should not be possible...
> Do you mean _MMPBSA_complex_gb.mdout.0?
>
>
> > Interestingly, it is the same error message as this message:
> >
> > http://archive.ambermd.org/201205/0651.html
> >
> > We have tried Jason's suggestion, which is *"add a space before the
> &cntrl
> > and the / character at the end of that file (you can use -make-mdins to
> > generate the MDIN files, change them, and then use the same command-line
> > with -use-mdins instead of -make-mdins to use your modified
> > copies).".* However, we add a space before the &general instead of the
> > &cntrl in the
> > mmpbsa.in file. The same error message occurs.
> >
>
> Putting a space in the MMPBSA.py input file has no effect, i was talking
> about adding a space to the &cntrl namelist of _MMPBSA_gb.mdin file (but it
> must have been written for sander). I don't think this should have been
> necessary...
>
>
> > We try to use Bill's suggestion
> > here<http://archive.ambermd.org/201205/0651.html>
> >
> > "I believe that you should be able to remove 'radiopt=0' from the &pb
> > section all of the mdin files created by MMPBSA.py (one of the complex,
> > receptor, and ligand). Afterwards, re-run the calculation with the
> > -use-mdins flag and you shouldn't see this error anymore. "
> >
> > So we edit _MMPBSA_gb.mdin like the following and try again, the same
> > error message still occurs.
> >
> > GB
> > saltcon = 0.1
> > gbsa = 1
> > extdiel = 78.3
> > surften = 0.0072
> > rgbmax = 25.0
> > igb = 7
> >
>
> Ugh. How is this possible, either? igb=7 doesn't exist in NAB (yet), so
> MMPBSA.py should use sander (and it should do so whether or not
> use_sander=1 is present in the input file). Furthermore, MMPBSA.py
> shouldn't even look for _MMPBSA_dummycomplex.inpcrd if it's using NAB, so
> how you got the original error message is puzzling.
>
> At this point I'm completely lost. I'm unsure of exactly what you did,
> what version you're using, what changes you've made to which files and
> when, etc...
>
> If you have made any changes to the source code, undo them. Go back to the
> original input file you had:
>
> Input file for running mmPBSA
> &general
> keep_files=2,use_sander=1,
> /
> &gb
> igb=7, saltcon=0.100
> /
>
> See if you still get the &cntrl namelist not found error message in the
> _MMPBSA_complex_gb.mdout.0 file. If yes, please post the _MMPBSA_gb.mdin
> file here. *This* file (_MMPBSA_gb.mdin) should be changed so that there
> is a leading space in front of &cntrl and /, which begin and terminate the
> namelist, respectively (maybe). I can't help much more than this since I
> can't actually reproduce any of the behavior you're seeing (so I can only
> speculate about what is going wrong).
>
> Also make sure the MMPBSA.py tests pass. You can go to
> $AMBERHOME/AmberTools/test/mmpbsa_py and type "make test". Do any of those
> tests fail?
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
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Received on Wed Feb 20 2013 - 11:30:02 PST
