Thank you Kenneth,
I think the problem lies with cpptraj v.15. It simply does not strip the solvent molecules.
Best wishes
George
> On 10 Aug 2015, at 22:30, Kenneth Huang <kennethneltharion.gmail.com> wrote:
>
> That's very possible, since I don't think that particular error message is
> usually associated with MMPBSA.
>
> I meant are there the appropriate number of numbers present? The error
> message says that it's finding more with a topology (complex?) than it
> expects, so it sounds like it's missing out on removing the solvent from
> that section. If it is, you should see noticeably more numbers compared to
> a protein only topology, since you have all the extra water atoms adding
> onto it. If so, you could try manually removing solvent and ions, though
> it'd be a time consuming workaround that you already circumvented.
>
> On Monday, August 10, 2015, George Tzotzos <gtzotzos.me.com
> <javascript:_e(%7B%7D,'cvml','gtzotzos.me.com');>> wrote:
>
>> 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
>>>>> here could not dream of heaven?
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Received on Mon Aug 10 2015 - 13:00:03 PDT
