Yes, it works the way you suggested. Thanks Bill!
Qiong
On Tue, May 22, 2012 at 9:40 PM, Bill Miller III <brmilleriii.gmail.com>wrote:
> 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 - 19:30:03 PDT
