search

Valdes-Tresanco-MS / gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/
GNU General Public License v3.0
226 stars 66 forks source link

[Question]: Prot-Memb-CHARMM decomp result interpretation #395

Closed lmk328 closed 1 year ago

lmk328 commented 1 year ago

My Question is...

Hi, I recently ran a "Prot-Memb-CHARMM" system according to your configuration https://valdes-tresanco-ms.github.io/gmx_MMPBSA/v1.5.6/examples/Protein_membrane_CHARMMff/. I found that in the FINAL_DECOMP_MMPBSA.dat, "Non-Polar Solv." column is all zero, which should be not true for such a system, as I suppose. I want to know how to interpret the real contributions of all the different terms per residue, according to the data file I have. Another issue is the high ΔEDISPER. I am trying to resolve this problem through your instructions, namely using "inp=1" and "use_sav=0", with other parameters unchanged. Here is the result and log files. Thank you very much! CXCR2_DIMER_CP_29.zip

Valdes-Tresanco-MS commented 1 year ago

Please, attach this file since it not included in the zip one

lmk328 commented 1 year ago

Sorry, something wrong happens when creating the zip file. Here is the file. 1st mmpbsa.zip

Valdes-Tresanco-MS commented 1 year ago

I don't remember exactly why this happens. I think it is because since the membrane is being approximated implicitly there is no way to estimate which residues interact directly with the solvent and so it is not computed. These are useful approximations for comparative analysis, but not for absolute contribution calculations. Decomposing the solvation energy in this case, should not give accurate results. Depending on your objective, you could compare the electrostatic, van der Waals, and polar contributions of solvation, which are usually the most notable. It is difficult to be absolutely certain of the values you compute in these cases.