[gmx-users] Starting residue "XXX"in chain not identified as Protein/RNA/DNA.

[Md. Imrul Reza Shishir]

Dear All
I have a structure file(.pdb) of single cellulose chain with Residue type
GLCB (beta-D-glucopyranosyl). I try to run the structure file with pdb2gmx
command and found this error.

I also attached the pdb file which i used.

"
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing proper dihedrals found on the same bond as a proper
dihedral
Residue 109
Sorting it all out...
Opening force field file ./gromos53a6.ff/aminoacids.hdb
Opening force field file ./gromos53a6.ff/aminoacids.n.tdb
Opening force field file ./gromos53a6.ff/aminoacids.c.tdb
Processing chain 1 (55 atoms, 2 residues)

*Warning: Starting residue UN15 in chain not identified as
Protein/RNA/DNA.Warning: Starting residue UN17 in chain not identified as
Protein/RNA/DNA.*
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
Checking for duplicate atoms....
Now there are 28 atoms. Deleted 27 duplicates.
Generating any missing hydrogen atoms and/or adding termini.
Now there are 2 residues with 28 atoms
Making bonds...
Warning: Long Bond (5-6 = 0.622482 nm)
Warning: Long Bond (6-7 = 0.814204 nm)
Warning: Long Bond (14-15 = 0.839694 nm)
Number of bonds was 29, now 29
Generating angles, dihedrals and pairs...
Before cleaning: 54 pairs
Before cleaning: 61 dihedrals
Making cmap torsions...
There are   44 dihedrals,    9 impropers,   39 angles
            48 pairs,       29 bonds and     0 virtual sites
Total mass 324.286 a.m.u.
Total charge -0.000 e
"




-- 
*Md Imrul Reza Shishir*
Master Student
*Inha University*
*CRC for NanoCellulose Future Composites*
36 Getbeol-ro, Yeonsu-gu
Incheon 21999
South Korea