Hannes Loeffler

Molecule numbers from AMBER parmtop/inpcrd start with 2

7

In the code below molecule numbers start from 2. OpenMMMD.py makes the assumption in centerSolute() that the solute is molnum 1. I get this with devel (commit 3371660dadf6fdc7c1095d69266529c7f4e12845). ``` import...

General suggestions for code cleanup/improvements

33

There is currently a lot of cruft growing in the code which is basically down to design choices. Here some suggestions: The parsers should be designed in a "polymorphic" fashion...

GIST: reference to bulk and column names

6

Hi, I am trying to find out which of the GIST columns are referenced to bulk water in order to compute the free energy. AMBER tutorial 25 suggests to compute...

I have updated the notebooks in the hope that this makes it more useful. I have fixed some questionable code, added timings, better structure, etc. I have also added code...

Hi, iSIM looks really interesting but I think it is rather undocumented and there is no installer in place. I have opened a PR with an updated notebook to fix...

Hi, it seems that the only way to specify the attachment point on the ligand in covalent docking is with SMARTS. It is certainly possible to do that but it...