Issue with Cellulose Conversion - Need Correct top-all36-carb.rtp and .prm Files

[Jayaprakash_H_M]

Hi everyone,

I’m following the tutorial shared here:

Equilibrating cellulose crytal to a realistic density with charmm36 force field

Hi everyone in the Material Science Discourse community, I’m currently working on simulating a cellulose uniaxial test and I’m reaching out to seek some advice from the community. I’ve built a cellulose data file using the CHARMM36 force field. The procedure followed the general steps outlined in this paper: (Molecular dynamics simulation of mechanical properties of carbon nanotube reinforced cellulose | Research Square). To achieve this, I used the cellulose-builder toolkit for constructing …

As part of the conversion process, the files top-all36-carb.rtp and top-all36-carb.prm are required. I attempted to use versions available online, specifically from this GitHub repository:

Charmm36_FF/toppar at master · ChayaSt/Charmm36_FF · GitHub

However, when I use these files, an extra bond appears within the cellulose structure, which is clearly incorrect.

Could someone kindly share the correct or working versions of top-all36-carb.rtp and top-all36-carb.prm that were used successfully for this cellulose system? Or advise on how to modify the existing ones to avoid the incorrect bond generation?

project.data (7.8 MB)
top_all36_carb.rtf (284.6 KB)
par_all36_carb.prm (152.6 KB)
project.pdb (940.2 KB)

[akohlmey]

@Jayaprakash_H_M

I’m following the tutorial shared here:

That is not a tutorial, but just another user like you asking for help

@Jayaprakash_H_M

However, when I use these files, an extra bond appears within the cellulose structure, which is clearly incorrect.

I am not so sure about that. You have a periodic system and the long bond like this would show up in VMD this way for bonds reaching across periodic boundaries. It appears, however, that your box dimensions are not proper for that and there are significant gaps between periodic images.

@Jayaprakash_H_M

Could someone kindly share the correct or working versions of top-all36-carb.rtp and top-all36-carb.prm that were used successfully for this cellulose system?

I don’t think those are the problem here.

@Jayaprakash_H_M

I attempted to use versions available online, specifically from this GitHub repository:

Charmm36_FF/toppar at master · ChayaSt/Charmm36_FF · GitHub

Those are for certain not the original files. The canonical location for obtaining the official CHARMM force field parameters is on Alex Mackerell’s homepage.

https://mackerell.umaryland.edu/charmm_ff.shtml

[Jayaprakash_H_M]

@akohlmey

Those are for certain not the original files. The canonical location for obtaining the official CHARMM force field parameters is on Alex Mackerell’s homepage.

Warning: bond parameter 1 for [NC311 NC311 ] was not found
Info: converting angles
Warning: angle parameter 1 for [NC311 NC311 NC311 ] was not found
Info: converting dihedrals
Warning: dihedral parameter 1 for [NC311 NC311 NC311 NC311 ] was not found
Info: converting impropers
Info: conversion complete

this is the output when iam using updated version of .prm and .rtf files
##########################################################################

When i used the files from here Charmm36_FF/toppar at master · ChayaSt/Charmm36_FF · GitHub
conversion worked but as mentioned previously there is an line passing across the cellulose

Any help to sort this out