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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Tue May 22 2012 - 10:30:09 PDT
