[gmx-users] Question Regarding Hydrogen Database Error

[Justin Lemkul]

On 2/4/17 8:21 PM, Elise White wrote:
> 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."
>

This means that the atom names in the input .pdb file do not match what you have 
in the .rtp file.  Change the atom names in the .pdb file so that they match.

-Justin

> 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/
> gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/aminoacids.r2b
>
> Reading 2MZ7_AA.pdb...
>
> WARNING: all CONECT records are ignored
>
> Read 'STRUCTURE OF TAU(267-312) BOUND TO MICROTUBULES', 347 atoms
>
> 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/
> gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/atomtypes.atp
>
> Atomtype 64
>
> Reading residue database... (gromos53a6_atb)
>
> Opening force field file /usr/local/bin/../Cellar/
> gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/aminoacids.rtp
>
> 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
> dihedral
>
> Residue 109
>
> Sorting it all out...
>
> Opening force field file /usr/local/bin/../Cellar/
> gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/aminoacids.hdb
>
> Opening force field file /usr/local/bin/../Cellar/
> gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/aminoacids.n.tdb
>
> Opening force field file /usr/local/bin/../Cellar/
> gromacs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/aminoacids.c.tdb
>
>
> 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
>
> 2
>
> Start terminus ACE-266: None
>
> Select end terminus type for NMA-312
>
>  0: COO-
>
>  1: COOH
>
>  2: None
>
> 2
>
> 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.
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================