Thank you very much Jason for your answer. You were right, I was not
including the LIG number in print_res.
Best regards
Alfredo
> What is your MMPBSA.py input file? My guess is that you defined a print_res that does not include the ligand residue, which may not be properly treated in MMPBSA.py...
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
> On Apr 11, 2012, at 10:03 AM, Alfredo Quevedo<alfredoq.fcq.unc.edu.ar> wrote:
>
>> Good morning. I am trying to perform residue decomposion analysis with
>> MMPBSA.py. I cant get the calculation to finish (it hangs up in the
>> ligand section). I inspected the input files and found that all energy
>> calculations are ok, but in the _MMPBSA_gb_decomp_lig.mdin file, the
>> "Residues to print" section is empty (posted below). I think that this
>> originates that the decomposition cant be performed.
>>
>> _MMPBSA_gb_decomp_lig.mdin file:
>>
>> File generated by MMPBSA.py
>> &cntrl
>> nsnb=99999, ntb=0, surften=0.0072,
>> extdiel=80.0, ncyc=0, cut=999.0,
>> gbsa=2, saltcon=0.15, imin=5,
>> idecomp=2, igb=5,
>> /
>> Residues considered as LIG
>> LRES 1 1
>> END
>> Residues to print
>> RES
>> END
>> END
>>
>>
>> The compiled test run is OK, that is to say that residues in the above
>> file are printed Ok. Any suggestion on were to look why the residue in
>> my specific case is not printed,
>> thank you very much in advance for the help,
>> best regards
>> Alfredo
>>
>>
>> --
>> ************************************************************************
>> Dr. Mario Alfredo Quevedo.-
>> Departamento de Farmacia.-
>> Facultad de Ciencias Qu?micas.-
>> Universidad Nacional C?rdoba.-
>> 5000 C?rdoba, Argentina
>> TE: 54351 4334163 Ext: 106
>>
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>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
--
************************************************************************
Dr. Mario Alfredo Quevedo.-
Departamento de Farmacia.-
Facultad de Ciencias Químicas.-
Universidad Nacional Córdoba.-
5000 Córdoba, Argentina
TE: 54351 4334163 Ext: 106
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Received on Wed Apr 11 2012 - 13:00:04 PDT
