Alanine Scanning Error (1Q->1A)

[Muhamad Alif Bin Che Nordin]

Hi team!

I am not too sure whether this issue have been addressed before but i hope you guys can help me out.

We tried to introduce a mutation 1Q->1A to a scFv using gmx_MMPBSA alanine scanning and it produced the error message. We are able to mutate on third amino acid 3Q->3A. Please help me to understand this issue and appreciate your help on how to proceed from this.

pls find the link attached files.

Thanks.

[Mario Sergio Valdes]

Version v1.4.3 had some problems with alanine scanning. Please use the latest version. 

Note, that the results are the same between versions, but recent versions have improved performance and fixed these bugs.

Before using the latest version, please review the documentation as it has several changes.

To be sure, I did the calculation with your system and noticed several problems:
- Even the most recent version has a small problem and that is that gmx_MMPBSA_ana does not recognize the mutant, because it is N-terminal. I have already made a PR (https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/pull/276) that includes the solution, so I will let you know as soon as it is ready for your calculation (under review ans test).
- The trajectory has PBC and consequently, the energy changes abruptly. Please check this section to remove them. (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/gmx_MMPBSA_running/#before-running-gmx_mmpbsa)

I will be in touch

Mario S.

[Mario Sergio Valdes]

Sorry for the late reply, I completely forget it.

You can install the latest dev version with the problems solved

python -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA