Crosslinking MPD-TMA using bond/react

LAMMPS LAMMPS General Discussion
1

Hello! I am trying to crosslink MPD and TMA using “fix bond/react”. In my pre-reacted and post-reacted files I have 37 and 34 atoms. During the crosslinking process, unreacted MPD amide groups within 4.5 ̊A of an unreacted TMA carboxyl group (amide nitrogen to carboxyl carbon distance) “react” to form a crosslink. Moreover, three atoms of HA (MPD amide), OH and HO (TMA) are deleted during crosslinking. When I run my input file, I get an error saying that “ERROR on proc 0: Bond/react: Number of equivalences in map file must equal number of atoms in reaction templates (…/fix_bond_react.cpp:3779)”. I would highly appreciate any suggestions.

Best,
Majid
mpd_tma_map.txt (2.0 KB)
input_mpd_tma_crossLinking.in (2.3 KB)
pre_reacted_mpd_tma.data (5.5 KB)
post_reacted_mpd_tma.data (5.0 KB)
MPD_TMA_crosslinked_FULL.data (140.4 KB)

2

For questions on fix bond/react you just mention @jrgissing in your post so he notices sooner.

3

Deleted atoms should be included in your post-reaction template, in which they cannot be connected to non-deleted atoms. So, if you delete three atoms and create three atoms, your post-reaction template should have three more atoms than your pre-reaction template. The equivalences section should have exactly as many atoms as the pre-reaction template.

Also, there are quite a few typos or instances of incorrect formatting in your map file. I would suggest looking at example map files here: examples/PACKAGES/reaction