[gmx-users] Cellulose topology file

[Iman Katouzian]

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
the structure was run successfully in Gromacs and the run was OK.
Could you please tell me what I'm doing wrong.
Thanks

-- 

*Iman Katouzian*

*Ph.D.** candidate of Food Process Engineering*

*Faculty of Food Science and Technology*

*University of Agricultural Sciences and Natural Resources, Gorgan, Iran*