>Do you have the same problem without asking for alanine scanning?
No, I don't.
> Is the above the entire error message?
This is the entire error message :
File "/home/amber16/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py", line 876, in _validate
raise PrmtopError('Complex natom != receptor natom + ligand natom')
PrmtopError: Complex natom != receptor natom + ligand natom
Exiting. All files have been retained.
Is it possible, instead of following the alanine scanning tutorial, to calculate the free energy of a mutate protein-protein complex just as the tutorial for a non-mutated complex?
________________________________
De: David A Case <david.case.rutgers.edu>
Enviado: terça-feira, 24 de abril de 2018 22:15
Para: AMBER Mailing List
Assunto: Re: [AMBER] Issue running alanine scanning
On Tue, Apr 24, 2018, Núbia Prates wrote:
>
> I am trying to run an alanine scanning calculation on the binding free
> energy of protein-protein complexes.
>
> PrmtopError: Complex natom != receptor natom + ligand natom*
>
> I verified the prmtop file of the complex, and it have the same atom
> numbers as the sum between receptor.prmtop and ligand.prmtop atoms.
Do you have the same problem without asking for alanine scanning? Is
the above the entire error message? You may have to modify whatever
scripts you are using to print the three natom numbers it is complaining
about, which may help in tracing down the problem.
....dac
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Received on Wed Apr 25 2018 - 12:30:03 PDT
