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
>>
>
>
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Received on Fri May 18 2012 - 13:00:03 PDT
