[gmx-users] Question Regarding Hydrogen Database Error

[Elise White]

Dr. Lemkul,

I have thoroughly inspected the contents of my PDB file and I am unsure
of where the naming issue you suggested is in regard to the CH3 atom.
The NMA group looks like the following:

ATOM    712  CA  NMA A 312A     11.567 -11.364  -9.880  1.00  0.00
     C
ATOM    713  HA1 NMA A 312A     12.057 -10.586 -10.507  1.00  0.00
  H
ATOM    714  HA2 NMA A 312A     11.526 -11.024  -8.821  1.00  0.00
    H
ATOM    715  HA3 NMA A 312A     12.148 -12.312  -9.934  1.00  0.00
   H
ATOM    716  N     NMA A 312A     10.216 -11.586 -10.377  1.00  0.00
     N
ATOM    717  H     NMA A 312A      9.618 -12.263  -9.928  1.00  0.00
       H

*I should probably have mentioned before that this capping group was added
using Maestro 11's protein preparation wizard from Schrodinger*

My .rtp entry is exactly what you suggested earlier on -

[ NMA ]
 [ atoms ]
    CA   CH3   0.000         1
     N     N      -0.310         2
     H     H       0.310         3
 [ bonds ]
     N     H
     N    CA

I have essentially tried everything I can think of in regard to fixing this
and am hoping
you might have some useful insight on how to proceed.







On Sat, Feb 4, 2017 at 8:21 PM, Elise White <elisenwhite at gmail.com> 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."
>
> 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/groma
> cs/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/groma
> cs/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/groma
> cs/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/groma
> cs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/aminoacids.hdb
>
> Opening force field file /usr/local/bin/../Cellar/groma
> cs/5.1.1_1/share/gromacs/top/gromos53a6_atb.ff/aminoacids.n.tdb
>
> Opening force field file /usr/local/bin/../Cellar/groma
> cs/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-20160831-84924-1r
> fxk36/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.
>
>