[gmx-users] Error regarding missing hydrogen atoms

[Vishal Pandya]

Hello Gromacs Users,

I have been trying to run a simulation of PTM residues which has NAG, BMA,
MAN, etc glycosylated residues in my protein. First, I would like to ask
does anyone has .hdb file for such molecules for charmm22* or charmm36 ff
as I am having following error:

*WARNING: atom H1 is missing in residue NAG 2345 in the pdb file*
*         You might need to add atom H1 to the hydrogen database of
building block NAG*
*         in the file merged.hdb (see the manual)*

*WARNING: atom O1 is missing in residue NAG 2345 in the pdb file*

*WARNING: atom HO1 is missing in residue NAG 2345 in the pdb file*
*         You might need to add atom HO1 to the hydrogen database of
building block NAG*
*         in the file merged.hdb (see the manual)*

*WARNING: atom H5 is missing in residue NAG 2345 in the pdb file*
*         You might need to add atom H5 to the hydrogen database of
building block NAG*
*         in the file merged.hdb (see the manual)*


*WARNING: atom H2 is missing in residue NAG 2345 in the pdb file*
*         You might need to add atom H2 to the hydrogen database of
building block NAG*
*         in the file merged.hdb (see the manual)*

*WARNING: atom HN is missing in residue NAG 2345 in the pdb file*
*         You might need to add atom HN to the hydrogen database of
building block NAG*
*         in the file merged.hdb (see the manual)*

I do have a .rtp pertaining to its bonds, impropers, atoms but just to make
it future-proof to use pdb2gmx, I would like to have it.

Cheers,
Vishal