[gmx-users] Cellulose topology file

[Justin Lemkul]

On 10/6/19 9:01 AM, Iman Katouzian wrote:
> Iman Katouzian <imaneternity at gmail.com>
> 4:07 PM (23 minutes ago)
> to gromacs.org_gmx-users
> Good day.
> I have a pdb file for nanocellulose and as I run the first command in
> Gromacs using
> gmx pdb2gmx -f Cellulose.pdb
> I encounter the following error :
> Warning: Starting residue UN15 in chain not identified as Protein/RNA/DNA.
> This chain lacks identifiers, which makes it impossible to do strict
> classification of the start/end residues. Here we need to guess this residue
> should not be part of the chain and instead introduce a break, but that will
> be catastrophic if they should in fact be linked. Please check your
> structure,
> and add UN1 to residuetypes.dat if this was not correct.
>
> Disabling further warnings about unidentified residues at start of chain.
> Problem with chain definition, or missing terminal residues.
> This chain does not appear to contain a recognized chain molecule.
> If this is incorrect, you can edit residuetypes.dat to modify the behavior.
> 8 out of 8 lines of specbond.dat converted successfully
>
> It seems that Gromacs does not recognize the residues but in a recent paper

You can't supply pdb2gmx with something named "UN" or "UNK," which many 
programs produce to indicate some "unknown" or non-standard residue. 
Cellulose is just a polymer of beta-D-glucose, which many force fields 
support. Your residues need to be named accordingly (e.g. BGLC or GLCB, 
depending on the force field, so check the .rtp file) and the atoms all 
need to be named correctly. Terminal sugars (reducing and non-reducing 
end) need to be defined differently because they do not have 1-4 
linkages, instead they have complete -OH groups.

> the structure was run successfully in Gromacs and the run was OK.

You should contact the corresponding author of the publication if you 
are having issues reproducing what they did.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================