Re: [AMBER] Python related problem running MMPBSA.py.MPI

From: Casalini Tommaso <tommaso.casalini.chem.ethz.ch>
Date: Wed, 10 Jun 2020 15:57:54 +0000

Dear Dr. Case,

I would like to add some details that may be useful.


As I mentioned, MMPBSA.py is fine.


When I use MMPBSA.py.MPI, the program correctly generates the .mdcrd files for the trajectory post processing (that is, it generates the _MMPBSA_complex.mdcrd.x files) and also it starts generating the files that contain the results for each frame that is, _MMPBSA_complex_pb_mdout.x files.


Essentially, everything stops before any number is written; this is what I obtain:


Reading parm file (Complex.prmtop)
title:
default_name
     Parameter topology includes 10-12 terms:
     These are assumed to be zero here (e.g. from TIP3P water)
        mm_options: e_debug=3
        mm_options: ipb=2
        mm_options: inp=1
        mm_options: epsin=4.000000
        mm_options: epsout=80.000000
        mm_options: smoothopt=1
        mm_options: istrng=150.000000
        mm_options: radiopt=0
        mm_options: dprob=1.400000
        mm_options: iprob=2.000000
        mm_options: npbopt=0
        mm_options: solvopt=1
        mm_options: accept=0.001000
        mm_options: maxitn=1000
        mm_options: fillratio=4.000000
        mm_options: space=0.500000
        mm_options: nfocus=2
        mm_options: fscale=8
        mm_options: bcopt=5
        mm_options: eneopt=2
        mm_options: cutnb=0.000000
        mm_options: sprob=1.400000
        mm_options: cavity_surften=0.005000
        mm_options: cavity_offset=0.000000
Processing ASCII trajectory (_MMPBSA_complex.mdcrd.0)

Processing frame 1
      iter Total bad vdW elect nonpolar EPB frms

I thank again for the support!
Tommaso


________________________________
Da: Casalini Tommaso <tommaso.casalini.chem.ethz.ch>
Inviato: mercoledý 10 giugno 2020 17:37:07
A: AMBER Mailing List
Oggetto: Re: [AMBER] Python related problem running MMPBSA.py.MPI

Dear Dr. Case,

I thank you for your quick reply.


I tested MMPBSA.py and everything went well.


With my best regards,

Tommaso

________________________________
Da: David A Case <david.case.rutgers.edu>
Inviato: mercoledý 10 giugno 2020 17:31:25
A: AMBER Mailing List
Oggetto: Re: [AMBER] Python related problem running MMPBSA.py.MPI

On Wed, Jun 10, 2020, Casalini Tommaso wrote:
>
>I am trying to run a MMPBSA.py.MPI calculation.
>
>I am using the last AmberTools version and I have employed python 3.6.0
>version when I installed it (in other words, I have used the flag
>--with-python=path_to_my_python3.6).

Can you check if running short run with MMPBSA.py itself works or fails?
That would help isolate the problem.

...thx...dac


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Received on Wed Jun 10 2020 - 09:00:05 PDT
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