camattelaer

> we need it for PhD too Just wanted to confirm. I am trying to reproduce my PhD thesis LaTex template in typst, but it was a necessity to have...

I'm encountering the same error being spammed in terminal output when performing geometry optimizations. Can't access xtb/conda versions right now, but if required for debugging i can look them up.

Hi Thanks for this very fast reply. Just to be clear I do not expect you to take actions so fast. At first glance, the atom mask should be modified...

I think you overlooked you also need H from NH in the backbone, i put it after N in my initial reply for logical ordering: > ` com_input['gb']['qmmask'] = f"({com_input['gb']['qmmask']}...

thank you very much for all your efforts. I will update, perform some tests and report back in a few days :) Kind regards CA

Ok, so I already encountered an issue: apparently in the mol2 file of the ligand, atom names such as N, H, C, O can also exist. if the input qmmask...

ok perfect. Thanks again I will do some tests and report back in due time :) kind regards CA

Hey guys, just wanted to mention that I'm currently not seeing an issue with the manual mask selection! Thank you for all your help on this issue. I do have...

``` # packages in environment at /home/camattelaer/Programs/anaconda3/envs/gmxMMPBSA: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge acpype 2023.10.27 pyhd8ed1ab_0 conda-forge ambertools 21.12 py39hc630cb1_0 conda-forge amberutils...

i would just like to add that i came here because the current conda package does not contain this patch. First time installation today in a new environment through conda-forge...