gmx_MMPBSA

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### In which tool? gmx_MMPBSA ### New Feature The sander program has the capability to run QM/MM simulations with the quantum chemical code QUICK (QUantum Interaction Computational Kernel) shipped along...

marioernestovaldes

[ENH]: qm atom mask selection

11

### In which tool? gmx_MMPBSA ### New Feature Currently qmmask selection is based on full residues, either directly via residue number or within specific distance of the ligand. Additional option...

camattelaer

[Question]: Why is my △TOTAL positive?

10

### My Question is... I check the trajectory. The molecules can stay very stable in the pocket and bind to the protein very well. However, the △TATOL=188.21kcal/mol, and the △EEL=0kcal/mol....

yuqingxiong96

[Question]: positive ΔG binding

3

### My Question is... Hello, in 2 out of 3 of my calculations, although ΔTOTAL is negative, binding ΔG is positive. Would you please tell me if there is any...

niloufar1993

[Bug-gmx_MMPBSA_ana]: qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found

1

### Bug summary I encountered issues while trying to use gmx_MMPBSA_ana, and it seems to not function properly. I attempted to follow the steps outlined in https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/208, but it did...

WANJIAL

[Question]: My molecule has two parts, A and B. I want to calculate the interaction between AB, but I don't want to consider the AB interaction within the same molecule. What should I do

2

### My Question is... My molecule has two parts, A and B. I want to calculate the interaction between AB, but I don't want to consider the AB interaction within...

kkivg

gmx editconf failed when querying ./com_traj.xtc in conda environment

22

### Bug summary I installed gmx_MMPBSA via conda and the version is v1.6.1, my python version is python 3.9.17 and I'm using Ubuntu 22.04.1, I have read the issue350, issue352...

kolmorgan

[ENH]: Decomp option to show only ligand-receptor interactions

1

### In which tool? gmx_MMPBSA ### New Feature It would be nice to be able to suppress the ligand-ligand and receptor-receptor interactions displayed in the decomposition when done pairwise. I'm...

wrmartin

### Bug summary pandas 1.2.2 seems broken. This change was made at #360. I fixed my project install by pinning gmx-mmpbsa (` gmx-mmpbsa ==1.6.1`). ### Terminal output ```bash gcc -pthread...

pgbarletta

### In which tool? gmx_MMPBSA_ana ### New Feature Better describe the panels ### Description Currently, the description of the panels is extremely poor and sometimes the elements are not even...

Valdes-Tresanco-MS