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
>
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Received on Tue May 22 2012 - 07:30:05 PDT
