Dr. Fabian Grunewald

Currently polyply assumes all residues are unique. That is mostly true but not quite at least at the all-atom level. For example, there might be a hydrogen extra or less...

@csbrasnett this PR should fix the issue with the residue names; I think it is about time that we added this functionality

@cesar-lopez-bau that sounds exciting! Are you going to share your CHARMM implementation at some point? To address your problem I've created a discussion thread (https://github.com/marrink-lab/polyply_1.0/discussions/353) with an example on how...

@tnozturk martini22 currently doesn't support protonation at least in martinize2

@pckroon the current state is that I think it correctly interprets the chirality but there is no way I can figure out how to get an absolute assignment from this,...

Hi @Jonifrc312, Glad to hear that you like polyply. The sequence you intend to use is indeed a bit awkward to generate with gen_seq, which is why we are working...

@Jonifrc312 please note that I adjusted the code. I wasn't paying enough attention this morning to the sequence. To get different length you need to change the 10 in this...

@Jonifrc312 glad to hear! You probably used `+` and `++` as prefix in the links; Since your resids are non-continous anymore you need to change to `>` `>>` so just...

Hi @Jonifrc312, I see! This problem is more a polyply than cgsmiles problem but the solution is quite easy: Flip the A and B in the cgsmiles string and use:...

@Jonifrc312 glad to hear and good catch! Of course the atomnames have to match and might get overwritten in this case. I wasn't considering this issue. I'll keep it in...