Only got the .psf file

[Fxzhou0919]

I would like to ask a question, I wrote a library .txt file based on the template under the libraries folder, I wanted to generate a lignin structure, but in the end, I only got the .psf file in my directory. Hence, I was wondering how to solve it. Many thanks again and I appreciate your time and support! The contents of the library .txt are as follows：

STARTING NEW POPULATION..... ***** CHAIN #1**** MW: 1091.15 Branch: 0 Distance Metric: 9.64389 0 0 61 - 30 11 18 0 0 1 0 Monomer List: 1: 3 2: 3 3: 3 4: 3 5: 3 6: 3 7: 3 8: 3 9: 3 10: 3 11: 3 12: 3 13: 3 14: 3 15: 3 16: 3 17: 3 18: 3 19: 3 20: 3 21: 3 22: 3 23: 3 24: 3 25: 3 26: 3 27: 3 28: 3 29: 3 30: 3 31: 3 32: 3 33: 3 34: 3 35: 3 36: 3 37: 3 38: 3 39: 3 40: 3 41: 3 42: 3 43: 3 44: 3 45: 3 46: 3 47: 3 48: 3 49: 3 50: 3 51: 3 52: 3 53: 3 54: 3 55: 3 56: 3 57: 3 58: 3 59: 3 60: 3 61: 3

Bond List: Monomer_I Monomer_II Pos_Mon_I Bond_type 1 2 3 3 2 3 1 2 3 4 1 1 4 5 3 3 5 6 4 6 6 7 1 1 7 8 1 1 8 9 1 1 9 10 3 3 10 11 1 1 11 12 3 3 12 13 1 1 13 14 1 2 14 15 1 2 15 16 1 1 16 17 1 2 17 18 1 1 18 19 3 3 19 20 1 1 20 21 1 2 21 22 3 3 22 23 1 1 23 24 1 1 24 25 3 3 25 26 1 1 26 27 3 3 27 28 1 1 28 29 1 1 29 30 1 1 30 31 3 3 31 32 1 1 32 33 1 1 33 34 3 3 34 35 1 2 35 36 1 1 36 37 3 3 37 38 1 1 38 39 1 1 39 40 1 1 40 41 1 2 41 42 1 1 42 43 3 3 43 44 1 2 44 45 1 1 45 46 3 3 46 47 1 1 47 48 1 2 48 49 1 1 49 50 1 1 50 51 3 3 51 52 1 2 52 53 3 3 53 54 1 1 54 55 1 2 55 56 1 1 56 57 3 3 57 58 1 1 58 59 3 3 59 60 1 1 60 61 3 3 #

FOR ENTIRE POPULATION >> Mn: 6435.61 Mw: 23628.6 Branch: 0 Distance metric: 0.892635 0 0 61 - 30 11 18 0 0 1 0

[jvermaas]

Hi, this is the error I get when running your input:

Info)    Segments: 1
Info)    Fragments: 1   Protein: 0   Nucleic: 0
-0.4060033168643713
This isn't an integer...
Info) VMD for LINUXAMD64, version 1.9.4a55 (August 18, 2022)
Info) Exiting normally.

Basically, your structure is setup in such a way that the charge on the PSF isn't an integer, and LigninBuilder is refusing to go onward. This often happens if you make too many linkages to a specific atom on lignin. Making legal library files is HARD, which is why we have other ways of building up specific lignin polymers. If you already have a structure drawn, you might consider exporting the structure to a SMILES and then using that approach.

[jvermaas]

One thing I should add: if you REALLY want to see what it looks like, you'd need to comment out the exit line near line 330 in ligninbuilder.tcl