Hi Jason,
I ran MMPBSA.py.MPI successfully by copying "sander" from /home/Amber/amber11/bin to /home/Amber/amber12/bin, so that
MMPBSA could find sander. I can not be sure whether this is proper.
However, the output file FINAL_DECOMP_MMPBSA.dat became a mess which confused me.
Here is my input file, and I will attach FINAL_DECOMP_MMPBSA.dat in the email.
Per-residue GB and PB decomposition
&general
startframe=201, verbose=1,
strip_mask=":WAT:Cl-:CIO:Cs+:IB:K+:Li+:Na+:Rb+"
/
&gb
igb=5, saltcon=0.100,
/
&pb
istrng=0.100,
/
&decomp
idecomp=1,
dec_verbose=1,
/
I tried to set dec_verbose=3 and run the job again with -rewrite-output, but the program aborted with the following error:
KeyError: 'rismrun_std'
I compiled the serial vesion of AmberTools 12 with -nofftw3. Will this be the case?
Thanks.
Cao Yang,
Zhejiang University
At 2012-06-01 20:40:44,"Jason Swails" <jason.swails.gmail.com> wrote:
>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 - 06:30:03 PDT
