This has already been fixed in the developer version of MMPBSA.py and
likely will be a bugfix soon (and obviously fixed in all future releases of
MMPBSA.py). 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.
-Bill
On Tue, May 22, 2012 at 10:28 AM, Qiong Zhang <qiong.zhang.qzh.gmail.com>wrote:
> Thank you Bill !
> I did what you suggested, and it works well for decomposed MMGBSA.
> But for decomposed MMPBSA, there is another problem. I searched the
> mailing list, and it is the same as the one reported by Jason before.
> http://dev-archive.ambermd.org/201002/0017.html
>
>
> File generated by MMPBSA.py
> &cntrl
> cut=999.0, nsnb=99999, ntb=0,
> ipb=2, imin=5,
> idecomp=1, inp=2, igb=10,
> /
> &pb
> maxitn=1000, fillratio=4.0, radiopt=0,
> /
> Residues considered as REC
> RRES 2 36
> END
> Residues considered as LIG
> LRES 1 1
> END
> Residues to print
> RES 1 2
> END
> END
>
> And the sander mdout errors:
> 1. RESOURCE USE:
>
> --------------------------------------------------------------------------------
>
> | Flags:
> PB Info in pb_read(): igb has been overwritten by ipb
> PB Bomb in pb_read(): use of radi other than vdw sigma for
> np solvation dispersion/cavity is not supported!
>
> Prof. Ray Luo suggested to use pbsa instead of sander. Is it still a
> problem with the present use of Ambetools12 ? (I am using
> Amber11/Ambertools12, I am sure this error won't occur to Amber11/AT1.5 for
> decomposed MMPBSA.)
>
> Qiong
>
>
>
> On Tue, May 22, 2012 at 7:10 AM, Bill Miller III <brmilleriii.gmail.com>wrote:
>
>> This is the problem that I was having when I ran your system with my
>> version of AmberTools 12 and Amber 12. I believe this is an actual bug in
>> MMPBSA.py, but I will have to look into it further before to see if it
>> affects other processes or not. You will need to modify the file
>> $AMBERHOME/AmberTools/src/mmpbsa_py/MMPBSA_mods/calculation.py. Search for
>> every instance of the word 'dummy' in that file. There should be six
>> instances, all corresponding to the complex, receptor, and ligand
>> _MMPBSA_dummy*.inpcrd.1 files with a duplicate of each one. Simply remove
>> the ".1" from the end of each one of those, so that file should have
>> %sdummycomplex.inpcrd instead of %dummycomplex.inpcrd.1 (once again for the
>> complex, receptor, and ligand). Once you have done this, re-compile
>> MMPBSA.py by going to $AMBERHOME/AmberTools/src/mmpbsa_py/ and typing 'make
>> install.'
>>
>> This should fix your problem.
>>
>> -Bill
>>
>>
>> On Mon, May 21, 2012 at 8:43 PM, Qiong Zhang <qiong.zhang.qzh.gmail.com>wrote:
>>
>>> 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
>>>> > > > >
>>>> > > > _______________________________________________
>>>> > > > 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
>>>>
>>>
>>>
>>
>>
>> --
>> Bill Miller III
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-6715
>>
>
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
_______________________________________________
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Received on Tue May 22 2012 - 19:00:03 PDT
