Sofia Bariami

Hi Lester, thanks for looking at it. By taking a closer look to the protein files, I saw that all the residues of the protein are called "QUP", so probably...

For the record, parmed is able to load back the prm7 files as a system made of a single residue ``` In [1]: import parmed as pmd In [2]: pmd.load_file("QUBE_pro.prm7",...

I did that but I get this Value error: ` ValueError: No template found for residue 1 (QUP). This might mean your input topology is missing some atoms or bonds,...

Hello, an update on this issue: - By including TER records between the protein fragments, the residues (all named QUP) were not recognised: `ValueError: No template found for residue 1...

Also all of the protein fragments are named QUP, so that might be an issue too

I used another pdb file, with each aminoacid defined seperately. Now the generated prm files looks normal (at least the atom names): ``` %FLAG ATOM_NAME %FORMAT(20a4) H1 CH3 H2 H3...

The length of the prm file was because of a bug at my script that was reading the parameters from the xml file. The problem was found at the 5-membered...

Hi Lester, thank you very much. This is very helpful. I am indeed trying to use BioSimSpace to work with molecules that are parameterised with another forcefield, and since the...

you can find the files and the script here: https://github.com/SofiaBariami/qube_project/tree/master/merge_molecules @jmichel80 when you say to post code for the Amber ff case, do you mean to refer to the BSS...

Thanks for the clarifications Julien. 1. When it comes to Amber, two sets of prm7/rst7 files are read with [readMolecules()](https://github.com/michellab/BioSimSpace/blob/62a3d98ab91b4c93bbddcc4a406ee676fc33f9ff/python/BioSimSpace/IO/_io.py#L206), to form two `BioSimSpace._SireWrappers._system.System`. From these system, we can extract...