[gmx-users] Question Regarding Hydrogen Database Error

[Justin Lemkul]

On 2/5/17 9:09 AM, Elise White wrote:
> 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

Note that none of these HA* should be there.  You'll get other warnings about 
that unless you're using -ignh.

> 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.
>

It's probably the .hdb, if you copied what I posted directly:

NMA     1
1   1   H  N   -C  CH3

That's a typo as your methyl carbon is named CA, not CH3.  Check to see if 
that's what is causing it.

-Justin

>
>
>
>
>
>
> 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.
>>
>>

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

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

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