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
>
>
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Received on Tue May 22 2012 - 10:30:09 PDT
