Bug #2900

Updated by Mark Abraham 12 months ago

I have a dimeric protein with two cofactors. After getting it through pdb2gmx (with some effort) I obtained a new pdb-file, which I passed on to editconf to get a suitable box. The cofactors however vanished in the editconf step.

I then tried using gromacs 2016.3, and then editconf managed to handle the cofactors. I also noticed some differences in the pdb2gmx step, where 2019.1 required the two cofactors to have different residue numbers, even though they belonged to different chains, whereas 2016 needed no such workaround.

Note that while investigating this issue, we also found that pdb2gmx, solvate and insert-molecules no longer accepted .tpr files as input, which is now fixed.