Thank you Kenneth,
Tried it. I’m afraid it doesn’t work. When I re-run mmpbsa.py on the original topology (Dimer + Ligands) it runs without a problem.
> On 10 Aug 2015, at 20:23, Kenneth Huang <kennethneltharion.gmail.com> wrote:
>
> I could be a little off here, but the problem might be-
>
> strip_mask=:DE3:DE4:WAT:Na+
>>
>
> You can try the above to see if it's fixed the issue.
>
> Best,
>
> Kenneth
>
> On Mon, Aug 10, 2015 at 12:49 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> I’m dealing with a complex consisting of two protein chains (125 residues
>> each) and two ligands. I was able to calculate DeltaG of the complex.
>>
>> parminfo for the complex is:
>>
>>> parminfo
>> Topology complex_solv.prmtop contains 42239 atoms.
>>
>> I want to evaluate DeltaG of the two protein chains without the two
>> ligands (named DE3, DE4). I’ve used ante-mmpbsa.py to generate new
>> topologies for the unliganded complex.
>>
>> ante-mmpbsa.py -p complex_solv.prmtop -s :DE3,:DE4,:WAT,Na+ -c
>> complex.prmtop -r chainA.prmtop -m :1-125 -l chainB.prmtop --radii=mbondi2
>>
>>
>> New complex(ChainA+ChainB)
>> parminfo
>> Topology complex.prmtop contains 3984 atoms.
>> Title: default_name
>> 250 residues.
>>
>> For mmgbsa.py, I used the following input script:
>>
>> Input file for running PB and GB
>> &general
>> strip_mask = :DE3,:DE4,:WAT,Na+
>> endframe=10000, verbose=1, interval=10,
>> # entropy=1,
>> /
>> &gb
>> igb=2, saltcon=0.100
>> /
>> &decomp
>> idecomp=1,
>> dec_verbose=1,
>> /
>>
>> When I run
>> mpirun -np 4 MMPBSA.py.MPI -O -i decomp.in -o FINAL_RESULTS_MMPBSA.dat
>> -do FINAL_DECOMP__MMPBSA.dat -sp complex_solv.prmtop -cp complex.prmtop -rp
>> chainA.prmtop -lp chainB.prmtop -y *.nc
>>
>> I get the following error.
>>
>> AmberParmError: FLAG ATOMIC_NUMBER has 42239 elements; expected 3984
>> Error occured on rank 2.
>> Exiting. All files have been retained.
>> AmberParmError: FLAG ATOMIC_NUMBER has 42239 elements; expected 3984
>> Error occured on rank 3.
>>
>> I’m rather perplexed because the mmpbsa input script has the same strip
>> mask as ante-mmpbsa.py.
>>
>> Any suggestions would be most helpful
>>
>> Regards
>>
>> George
>>
>>
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>>
>
>
>
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> here could not dream of heaven?
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Received on Mon Aug 10 2015 - 11:00:03 PDT
