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
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 22 2012 - 09:30:12 PDT
