Gromacs .hdb format RU5 case study

User discussions
1

GROMACS version: 2025.3
GROMACS modification: No

Hi,

I am trying to understand .hdb file format to build modified residue. As a test, I am working on RU5 residue from Amber forcefield. I read relevant section from pdb2gmx but I am still confused about some notations, hope to receive some suggestions here.

Below is the entry of RU5 from “rna.hdb”

RU5     10
1       2       H5T     O5'     C5'     C4'                                                
2       6       H5'     C5'     O5'     C4'                                                
1       5       H4'     C4'     C5'     O4'     C3'                                        
1       5       H1'     C1'     O4'     N1      C2'                                        
1       1       H6      C6      N1      C5                                                 
1       1       H5      C5      C6      C4                                                 
1       1       H3      N3      C4      C2                                                 
1       5       H3'     C3'     C4'     C2'     O3'                                        
1       5       H2'1    C2'     C1'     C3'     O2'                                        
1       2       HO'2    O2'     C2'     C1'

First line is residue name, kind of hydrogen atoms. I guess first column is suggesting number of same kind of hydrogen, as H5’1 and H5’2 are same kind, first column mentions 2.

My query is:

  1. How the values in second column decided?
  2. A few lines have 5 atoms mentioned, are these all atoms 2 bonds away from hydrogen atom of interest (for e.g. H4’)?
  3. Also, just want to check, are there any tools to convert Parmed generated topology to rtp, and hdb entries. I came across Gromologist package, it is interesting, but somewhere it is mentioned that rtp generation is in beta phase.

Thanks in advance,

Mandar

2

Hi Mandar! By “relevant section of pdb2gmx”, do you mean this one? It should have all the information needed to understand the file format. In particular, the format is (# means number of):
[residue name] [#kinds of H]
[# H added] [method] [name of H type] [3-4 control atoms]

Sadly, can’t speak on tools because I haven’t used any. Hope this helps!

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4

Thanks, followed the same link, but missed the codes for hydrogen type.
If the H type is 5, I guess 4 control atoms need to be mentioned.

5

Yes, exactly.

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