Alanine scanning error on PRO to ALA and GLY to ALA mutation[protein-protein]

[JunYoung Shin]

hi everyone!

I perform alanine scanning for protein-protein, the following error occurred:

(error-1)

[INFO   ] Writing Normal Ligand AMBER topology...
[INFO   ] Building Mutant Complex Topology...
[ERROR  ] MMPBSA_Error Selecting residue A:PRO:107 can't be mutated. Please, define a valid residue....
           Check the gmx_MMPBSA.log file to report the problem.

(error-2)

[INFO   ] Writing Normal Ligand AMBER topology...
[INFO   ] Building Mutant Complex Topology...
[ERROR  ] MMPBSA_Error Selecting residue A:GLY:112 can't be mutated. Please, define a valid residue....
           Check the gmx_MMPBSA.log file to report the problem.

Of the 20 amino acids, only Gly and Pro can't be mutated to Ala.

How can I solve this problem?

[Mario Ernesto]

You are trying to mutate a proline residue by alanine and this is not supported in gmx_MMPBSA (same for glycine)... This is a "limitation" in the algorithm gmx_MMPBSA uses to generate the mutants, which is pretty simple and effective... This is somewhat justified in the fact that proline and glycine are "special" aminoacids often important to mantain certian structure... In your case, if you really want to mutate a proline residue, you could perform a new simulation with the structure with the alanine residue...

Hope this helps!

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