[gmx-users] Question Regarding Hydrogen Database Error

Elise White elisenwhite at gmail.com
Sun Feb 5 02:21:38 CET 2017

Dr. Lemkul,

Thank you very much for you help!

I just modified my aminoacids.rtp file and my .hdb file as you suggested
and tried running the protein through pdb2gmx just to ensure there weren't
any other errors.

Unfortunately, another error message has popped up now which says,
"Residue 48 named NMA of a molecule in the input file was mapped to an
entry in the topology database, but the atom CH3 used in that entry is not
found in the input file."

Do you have any suggestions as to how I can avoid this? I have attached
the full error message below.

  gmx pdb2gmx -f 2MZ7_AA.pdb -o 2MZ7_AA.gro -ignh -ter -ff gromos53a6_atb
-water spc

Using the Gromos53a6_atb force field in directory gromos53a6_atb.ff

Opening force field file /usr/local/bin/../Cellar/

Reading 2MZ7_AA.pdb...

WARNING: all CONECT records are ignored


Analyzing pdb file

Splitting chemical chains based on TER records or chain id changing.

There are 1 chains and 0 blocks of water and 48 residues with 347 atoms

  chain  #res #atoms

  1 'A'    48    347

All occupancies are one

Opening force field file /usr/local/bin/../Cellar/

Atomtype 64

Reading residue database... (gromos53a6_atb)

Opening force field file /usr/local/bin/../Cellar/

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

Residue 109

Sorting it all out...

Opening force field file /usr/local/bin/../Cellar/

Opening force field file /usr/local/bin/../Cellar/

Opening force field file /usr/local/bin/../Cellar/

Back Off! I just backed up topol.top to ./#topol.top.2#

Processing chain 1 'A' (347 atoms, 48 residues)

Analysing hydrogen-bonding network for automated assignment of histidine

 protonation. 71 donors and 63 acceptors were found.

There are 95 hydrogen bonds

Will use HISE for residue 268

Will use HISE for residue 299

Identified residue ACE266 as a starting terminus.

Identified residue NMA312 as a ending terminus.

8 out of 8 lines of specbond.dat converted successfully

Special Atom Distance matrix:

                  HIS268  CYS291

                   NE222   SG192

  CYS291   SG192   1.498

  HIS299  NE2254   2.400   1.077

Select start terminus type for ACE-266

 0: NH3+

 1: NH2

 2: None


Start terminus ACE-266: None

Select end terminus type for NMA-312

 0: COO-

 1: COOH

 2: None


End terminus NMA-312: None

Checking for duplicate atoms....

Generating any missing hydrogen atoms and/or adding termini.


Program gmx pdb2gmx, VERSION 5.1.1

Source code file: /tmp/gromacs-20160831-84924-1rfxk36/gromacs-5.1.1/src/
gromacs/gmxpreprocess/pgutil.c, line: 127

Fatal error:

Residue 48 named NMA of a molecule in the input file was mapped

to an entry in the topology database, but the atom CH3 used in

that entry is not found in the input file.

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