On Fri, Jun 1, 2012 at 12:58 AM, Cao Yang <muxiachuixue.163.com> wrote:
> Hi all,
>
> I installed AMBER11 and AmberTools 12 with all bugfix. In order to combine
> AMBER11 with AmberTools 12, I did the following commands before running
> MMPBSA.py:
>
> export AMBERHOME=/home/Amber/amber12
> export PATH=$PATH:$AMBERHOME/bin:/home/Amber/amber11/bin
>
> But MMPBSA aborted in my decompostion analysis with the error below:
> MMPBSA_Error: Could not find necessary program [sander]
>
> The reason may be that MMPBSA could not find sander in
> /home/Amber/amber12/bin.
> But I have added "AMBERHOME/bin:/home/Amber/amber11/bin" to my
> environment. Won't MMPBSA search sander in /home/Amver/amber11/bin? That
> confused me. This time, I just copy sander from /home/Amber/amber11/bin to
> /home/Amber/amber12/bin. And the job runs smoothly.
>
By default, MMPBSA.py only searches in $AMBERHOME/bin for executables,
since that's where it expects to find the programs that it is known to work
with. To search for programs outside this folder (and anywhere in the
PATH), add the variable "search_path=1" to the &general section of your
MMPBSA.py input file.
Also note that you should set dec_verbose=3 to get sander from Amber 11 to
work. You can change dec_verbose and run -rewrite-output to get the output
file you desire, but only dec_verbose=3 will allow the calculation to run
in the first place (unless you use -make-mdins, remove the dec_verbose
variable from all of the mdin files, then use -use-mdins).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Jun 01 2012 - 06:00:03 PDT
