error when calculating binding free energy

[li tao]

Dear marioe,

   I met an error with calculating binding free energy ,pls help me check it, and give me a solution, thanks a lot.

 By the way,  I used a protonated GLU when running MD, if it caused the error occurred during binding energy calculation. 

[Mario Ernesto]

Hello there!

Could you please send around the files you are using? (mmpbsa.in,  md01.tpr, index.ndx, md01-nojump.xtc (just a few frames) and AAA_gaff.mol2

Cheers!

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[li tao]

thanks a lot, these files have been attached. 

[Mario Ernesto]

I did use the mmpbsa.in attached (the only difference is the start and end frame given that the traj you sent has a few frames) and the following command:

gmx_MMPBSA -O -i mmpbsa.in -cs md01.tpr -ci index.ndx -cg 1 13 -ct 30frames.xtc -lm AAA_gaff.mol2

and it works fine...

are you using the last version of the program?

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[marioe911116]

to summarize as we talked about this offline:

for some systems with protonated residues (GLU, ASP,  etc), the stable version from PYPI can end in error... to fix this just upgrade gmx_MMPBSA with the following command:

amber.python -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA.git@25a02b8 --upgrade

cheers!

[Mario Sergio Valdes]

The current version (v1.4.3) contains the error that will be fixed for v1.5.0