[gmx-users] how to rename my hydrogens before pdb2gmx

Anderson, Amos Amos.Anderson at pfizer.com
Thu Jul 26 12:08:30 CEST 2018

Hi Gromacs users,

I’d like to use pdb2gmx on a structure to which I’ve added hydrogens I’d like to keep, that is, I don’t want to use –ignh, which is the typical recommendation I see. However, I’m finding that gromac’s hydrogen nomenclature isn’t one I’m familiar with.

Take PRO for example (the first one that fails in my pdb). The standard hydrogen names are:
which, for HB in V3, are HB2 and HB3.

In gromacs however, all the forcefields use HB1 and HB2 (grep pasted below). This naming choice is neither V3 nor V2 of the PDB’s nomenclature.

Has anybody worked out a map/utility I could use to rename my hydrogens to match what pdb2gmx would expect? Is the hydrogen nomenclature consistent across all forcefields?


/share/gromacs/top>  grep -A15 "\[ PRO \]" */*rtp | grep HB
amber03.ff/aminoacids.rtp-   HB1    HC           0.019352    9
amber03.ff/aminoacids.rtp-   HB2    HC           0.019352   10
amber94.ff/aminoacids.rtp-   HB1    HC           0.02530     9
amber94.ff/aminoacids.rtp-   HB2    HC           0.02530    10
amber96.ff/aminoacids.rtp-   HB1    HC           0.02530     9
amber96.ff/aminoacids.rtp-   HB2    HC           0.02530    10
amber99.ff/aminoacids.rtp-   HB1    HC           0.02530     9
amber99.ff/aminoacids.rtp-   HB2    HC           0.02530    10
amber99sb-ildn.ff/aminoacids.rtp-   HB1    HC           0.02530     9
amber99sb-ildn.ff/aminoacids.rtp-   HB2    HC           0.02530    10
amber99sb.ff/aminoacids.rtp-   HB1    HC           0.02530     9
amber99sb.ff/aminoacids.rtp-   HB2    HC           0.02530    10
amberGS.ff/aminoacids.rtp-   HB1    HC           0.02530     9
amberGS.ff/aminoacids.rtp-   HB2    HC           0.02530    10
charmm27.ff/aminoacids.rtp- HA HB 0.09 5
charmm27.ff/aminoacids.rtp- HB1 HA 0.09 7
charmm27.ff/aminoacids.rtp- HB2 HA 0.09 8
oplsaa.ff/aminoacids.rtp-   HB1    opls_140    0.060     2
oplsaa.ff/aminoacids.rtp-   HB2    opls_140    0.060     2

Repo uses the same names:

Program:     gmx pdb2gmx, version 2018.2
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 753)

Fatal error:
Atom HB3 in residue PRO 30 was not found in rtp entry PRO with 16 atoms
while sorting atoms.

For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

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