Kenneth, many thanks once again
I think the bug is with cpptraj v.15
I switched back to cpptraj v.13.24 and it works fine.
Concerning the FLAG ATOMIC_NUMBER portion, what exactly do you want me to check.
All prmtop files contain
%FLAG ATOMIC_NUMBER
%FORMAT(10I8)
Regards
George
> On 10 Aug 2015, at 21:43, Kenneth Huang <kennethneltharion.gmail.com> wrote:
>
> Huh. Have you tried checking the output prmtops from ante-MMPBSA itself?
> Specifically the FLAG ATOMIC_NUMBER portion, since it seems like a
> strip_mask issue here, but the error message might be saying that there
> might've been a hiccup somewhere with the input prmtops if your old ones
> are working fine.
>
> Best,
>
> Kenneth
>
> On Mon, Aug 10, 2015 at 1:37 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> 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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>> imprisoned
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>
>
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> here could not dream of heaven?
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Received on Mon Aug 10 2015 - 12:30:03 PDT
