I see. Thanks! :-))
Qiong
On Tue, May 22, 2012 at 1:11 PM, Jan-Philip Gehrcke <jgehrcke.googlemail.com
> wrote:
> Ha!
>
> Actually, Python is an interpreted language and the "source change"
> would have taken effect even before invoking the first 'make install' :-)
>
> Jan-Philip
>
>
> On 22.05.2012 19:05, Qiong Zhang wrote:
> > Hi Jan-Philip,
> > Thanks a lot for your explanation and suggestions!
> > I've tried Ambertools12. But we do not have amber12. And with
> > Amber11/Ambertools12, I've got another problem sent to the mailing list
> > earlier today.
> > For solution 1), I entered $AMBERHOME/AmberTools/src/mmpbsa_py/ and in
> > MMPBSA.py, change line 564 (for
> > me) from `sander = utils.which(prog)` to `sander =
> utils.which(prog,True)`,
> > tried to "make install". But the problem still exists. I checked
> MMPBSA.py
> > again and found that after "make install", line 564 in MMPBSA.py changed
> > back to `sander = utils.which(prog)` again. I tried to change line 604 in
> > MMPBSA.pypp in the same directory from `sander = utils.which(prog)` to
> > `sander = utils.which(prog,True)`, and now it works well !
> > Thanks again for your help! :)
> > Qiong
> >
> >
> >
> >
> > On Tue, May 22, 2012 at 12:25 PM, Jan-Philip Gehrcke<
> > jgehrcke.googlemail.com> wrote:
> >
> >> Hey Qiong,
> >>
> >> first of all, why don't you use AmberTools 12? :) Is your patch invalid
> >> against it?
> >>
> >> By default, MMPBSA.py from AT 1.5 unfortunately only searches
> >> AMBERHOME/bin for the sander binary. It ignores the environment's PATH
> >> variable. Hence, if you want to stick to AT 1.5, you have two options:
> >>
> >> 1) modify $AMBERHOME/AmberTools/src/mmpbsa_py/MMPBSA.py, line 564 (for
> >> me) from `sander = utils.which(prog)` to `sander = utils.which(prog,
> >> True)` (and consider performing the analogue change for MMPBSA.py.MPI).
> >>
> >> 2) link the sander executable of your choice into your $AMBERHOME/bin
> >> directory.
> >>
> >> Does this help?
> >>
> >> Jan-Philip
> >>
> >>
> >> On 22.05.2012 17:52, Qiong Zhang wrote:
> >>> Hi Jan-Philip,
> >>> Thanks for the reply. Now with the following settings:
> >>> export AMBERHOME=/home/user/amber11
> >>> export PATH=$PATH:/home/user/amber11/bin:/directory on cluster for
> >>> amber/amber11/bin
> >>>
> >>> `which MMPBSA` returns /home/user/amber11/bin/MMPBSA
> >>> `which sander` returns /directory on cluster for
> amber/amber11/bin/sander
> >>>
> >>> So there are all right now. But when running decomposed MMPBSA
> >>> calculations, "Error: sander could not be found!" still exists. So it
> >> seems
> >>> that the program can only search executables in $AMBERHOME/bin.
> >>>
> >>> How to do it in Ambertools1.5 for the program to find executables in
> the
> >>> full PATH when they can't be found in $AMBERHOME/bin?
> >>> In Ambertools12, there is a variable ‘search_path’ in the input file to
> >>> control this. But how about in Ambertools1.5 please? Thanks for any
> >> advice.
> >>>
> >>> Qiong
> >>>
> >>>
> >>> On Tue, May 22, 2012 at 11:21 AM, Jan-Philip Gehrcke<
> >>> jgehrcke.googlemail.com> wrote:
> >>>
> >>>> Hello Qiong,
> >>>>
> >>>> if `which MMPBSA` finds the wrong executable, the order of directories
> >>>> still is wrong in your PATH environment variable. Make sure that your
> >>>> new AMBERHOME directory appears in $PATH before any other
> Amber-related
> >>>> directories. By doing so, your shell will find and use the MMPBSA
> >>>> executable in your new AMBERHOME directory.
> >>>>
> >>>> You accomplish that via e.g.
> >>>>
> >>>> export AMBERHOME=/home/user/amber11
> >>>> export PATH=${AMBERHOME}/bin\:${PATH}
> >>>>
> >>>> This *prepends* your AMBERHOME/bin directory to your PATH.
> >>>>
> >>>> You have to make sure by yourself that after executing these lines no
> >>>> other script is prepending a 'wrong' directory to the PATH. In any
> case,
> >>>> if you still have problems, you should validate the order of directory
> >>>> occurrences in PATH manually:
> >>>>
> >>>> echo $PATH
> >>>>
> >>>> Hope this helps,
> >>>>
> >>>> Jan-Philip
> >>>>
> >>>>
> >>>>
> >>>> On 05/22/2012 04:59 PM, Qiong Zhang wrote:
> >>>>> export AMBERHOME=/home/user/amber11
> >>>>> export PATH=$PATH:$AMBERHOME/bin:/directory on cluster for
> >>>> amber/amber11/bin
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> 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
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
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> >>
> > _______________________________________________
> > AMBER mailing list
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Tue May 22 2012 - 10:30:10 PDT
