Atom not recognized, but clearly is in the pdb [pdb2gmx using Charmm36]

GROMACS version:
GROMACS modification: Yes/No

I’m trying to use pdb2gmx and the CHARMM36 force field. My PDB file (a parallelepiped crystal generated using Cellulose Builder) only contains BGLC residues (which I see is in the carb.rtp of the CHARMM36 force field) However, when I run pdb2gmx, I get this error:

**Fatal Error **
Residue 1 named BGLC of a molecule in the input file was mapped
to an entry in the topology database, but the atom O1 used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

I checked my pdb and there is O1 in the file (in some cellbiose units). However, there is no O1 in several other units - I believe these missing atom is expected because they are only part of glycosidic bonds. I think this is the problem, but is there any way around this? In VMD, the crystal is well constructed.


BGLC is a standalone glucose, not a residue in a chain with 1->4 linkages. AFAIK, we do not have suitably patched residues that reflect “internal” glucose units in a cellobiose chain. You would have to create these by applying the appropriate patches (referenced from the original CHARMM top_all36_carb.rtf file). The dehydration that occurs at the linkage requires changes to those atoms and their charges.

Hello Professor,

Thank you for your response. Let me see if I understand what you mean – so, the CHARMM36 only has carb parameters for the standalone glucose. The original top_all36_carb.rtf file, however, contains the necessary patches for the glucose linkages.

I see now in top_all36_carb.rtf that for equatorial-equatorial 1–>4 linkage patch for example, there is a deletion of the O1 – perhaps this explains the missing O1 in my pdb? So if I add this patch, it will not provide this error.

–! equatorial-equatorial 1->4 linkage
PRES 14bb 0.02 ! (i)1->4(i-1) equatorial at C1 and equatorial at C4
dele atom 1HO4
dele atom 2HO1
dele atom 2O1
ATOM 1C4 CC3161 0.09 !
ATOM 1O4 OC301 -0.36 !
ATOM 2C1 CC3162 0.29 !
BOND 1O4 2C1
IC 1C3 1C4 1O4 2C1 1.5009 110.76 81.86 121.00 1.3902 ! psi
IC 1C4 1O4 2C1 2O5 1.4560 121.00 -130.97 108.63 1.447 **! phi
IC 2O5 1O4 *2C1 2C2 1.4470 108.63 -122.09 110.89 1.5316
IC 2O5 1O4 *2C1 2H1 1.4470 108.63 121.92 111.32 1.0837

If I understand you correctly - I should go about creating these patches by copying the linkage patch from the top_all36_carb.rtf and adding the CHARMM36 .rtf file ? Then, I can go about utilizing this new “ff” using pdb2gmx? I wonder if I had to make any modifications to the other carb files in the CHARMM36 ff folder.

Thank you for your expert insight!

You cannot copy the patch into an .rtp file. You need to create an “internal” chain residue that applies the indicated modifications. Deletion of some atoms and reassignment of atom types/charges to create the version of BGLC that will be present in the chain.