Re: [AMBER] ante-mmpbsa.py: problem with the mask syntax

From: George Tzotzos <gtzotzos.me.com>
Date: Mon, 16 Mar 2015 16:59:49 -0300

Thank you Jason,

I hadnít stripped the trajectory of waters and ligands and this seems to have produced the problem.

Following your suggestion, I proceeded in two stages:

1. I stripped waters and ligands
2. I used the stripped trajectory and the new topologies produced by ante-mmpbsa.py using the script below:

mpirun -np 12 MMPBSA.py.MPI -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -cp subA-subB.prmtop -rp subA.prmtop -lp subB.prmtop -y stripped.nc

It didnít throw any error messages.

Cheers

George

On 16Mar, 2015, at 4:18 PM, Jason Swails <jason.swails.gmail.com> wrote:

> On Mon, Mar 16, 2015 at 3:12 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> Thank you Jason and Kenneth
>>
>> I used Kennethís script to get topologies stripped of waters and ligands
>> (Case 2). parminfo shows the prmtop files to be as expected. When I run
>> MMPBSA.py.MPI, it throws the following error
>> CalcError: /Users/3i521409/Programs/amber12/bin/cpptraj failed with prmtop
>> subA.prmtop!
>> Error occured on rank 9.
>> Exiting. All files have been retained.
>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 9
>>
>> Is there a way to troubleshoot this?
>>
>
> cpptraj is dying. Presumably because there is a mismatch in the number of
> atoms in the prmtop and the generated coordinate files. Did you remember
> to set strip_mask in your MMPBSA.py input file to get rid of your ligands
> as well as solvent? That's the most likely culprit based on what I know of
> your workflow.
>
> I would also suggest using MMPBSA.py in serial on 1 or 2 frames, and then
> scaling up once you get that to work.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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> AMBER.ambermd.org
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Received on Mon Mar 16 2015 - 13:30:02 PDT
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