Thanks Jason. The strip_mask modification helped.
Thanks.
On Thu, Sep 18, 2014 at 4:59 AM, Sourav Purohit <sour000.gmail.com> wrote:
> And one more information that I would like to share is that when I run the
> nmode calculation with the same set of topology files, I get a different
> error stating that the EXECTED NUMBER OF BOX CO-ORDINATES which is 3 or 6
> DOES NOT MATCH THE CO-ORDINATES DETECTED (4). Could this again be due to
> the strip_mask issue.
>
> Please comment on this.
>
> On Thu, Sep 18, 2014 at 4:53 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>> On Wed, Sep 17, 2014 at 7:18 PM, Sourav Purohit <sour000.gmail.com>
>> wrote:
>>
>> > I have two ions in my dry complex trajectopy file. I run the binding
>> energy
>> > calculations. I get the following error:
>> >
>> > Loading and checking parameter files for compatibility...
>> > mmpbsa_py_energy found! Using
>> > /home/suman/Downloads/amber14/bin/mmpbsa_py_energy
>> > cpptraj found! Using /home/suman/Downloads/amber14/bin/cpptraj
>> > Preparing trajectories for simulation...
>> > 3 frames were processed by cpptraj for use in calculation.
>> >
>> > Running calculations on normal system...
>> >
>> > Beginning GB calculations with
>> > /home/suman/Downloads/amber14/bin/mmpbsa_py_energy
>> > calculating complex contribution...
>> > File "/home/suman/Downloads/amber14/bin/MMPBSA.py", line 96, in
>> <module>
>> > app.run_mmpbsa()
>> > File "/home/suman/Downloads/amber14/bin/MMPBSA_mods/main.py", line
>> 218,
>> > in run_mmpbsa
>> > self.calc_list.run(rank, self.stdout)
>> > File "/home/suman/Downloads/amber14/bin/MMPBSA_mods/calculation.py",
>> line
>> > 79, in run
>> > calc.run(rank, stdout=stdout, stderr=stderr)
>> > File "/home/suman/Downloads/amber14/bin/MMPBSA_mods/calculation.py",
>> line
>> > 459, in run
>> > self.prmtop))
>> > CalcError: /home/suman/Downloads/amber14/bin/cpptraj failed with prmtop
>> > 1kf1e2_vac_now.prmtop!
>> > Exiting. All files have been retained.
>> >
>> >
>> > 1kf1e2_vac_now.prmtop is the dry complex topology which has two ions.
>> > Can you guess what the problem is??
>> >
>>
>> Yes, but all I can do is guess with the information you provided. I
>> suspect that you did not adjust strip_mask and MMPBSA.py stripped out the
>> atoms from the solvated trajectory. So the trajectories no longer match
>> the topology files.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
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>>
>
>
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Received on Wed Sep 17 2014 - 17:30:03 PDT
