[gmx-users] Missing H from residue

[Mark Abraham]

Jack Shultz wrote:
> Well I was just wondering if there was some porgram that could add
> this atom automatically. It looks like this "H" is missing. I supposed
> I could re-write the pdb file. It has all these non-standard
> Hydrogens. HB, HG and HT. Maybe I can just replace those.

Non-standard? H[ABGDEZ][123] are the H atoms for the heavy atom that is 
alpha through zeta to the backbone carbonyl.

> This is the residue in question
> 
> ATOM      1  N   GLU    32     -20.050   8.920  -4.700  1.00  0.00           N
> ATOM      2  CA  GLU    32     -19.847   8.507  -3.304  1.00  0.00           C
> ATOM      3  C   GLU    32     -20.807   7.451  -2.751  1.00  0.00           C
> ATOM      4  O   GLU    32     -21.843   7.183  -3.340  1.00  0.00           O
> ATOM      5  CB  GLU    32     -19.913   9.782  -2.416  1.00  0.00           C
> ATOM      6  CG  GLU    32     -18.641  10.678  -2.498  1.00  0.00           C
> ATOM      7  CD  GLU    32     -18.573  11.627  -1.334  1.00  0.00           C
> ATOM      8  OE1 GLU    32     -19.009  12.797  -1.488  1.00  0.00           O
> ATOM      9  OE2 GLU    32     -18.089  11.174  -0.257  1.00  0.00           O
> ATOM     10  HA  GLU    32     -18.845   8.057  -3.227  1.00  0.00           H
> ATOM     11  HB1 GLU    32     -20.805  10.368  -2.695  1.00  0.00           H
> ATOM     12  HB2 GLU    32     -20.026   9.493  -1.358  1.00  0.00           H
> ATOM     13  HG1 GLU    32     -17.724  10.072  -2.453  1.00  0.00           H
> ATOM     14  HG2 GLU    32     -18.628  11.255  -3.435  1.00  0.00           H
> ATOM     15  HT2 GLU    32     -19.381   9.526  -5.140  1.00  0.00           H
> ATOM     16  HT1 GLU    32     -20.892   8.644  -5.172  1.00  0.00           H
> 
> [boincadm at vps test]$ grep -A5 "GLU"
> /usr/local/gromacs/share/gromacs/top/ffamber99sb.*
> /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb:GLU        4
> /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-1  1       H
>  N       -C      CA

So here, for GLU, the H can't be constructed because there is no C from 
a preceding residue. Hence the need for NGLU per Justin's suggestion. 
However your grep should have found NGLU if you have a complete 
installation.

Mark

> /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-1  5       HA
>  CA      N       CB      C
> /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-2  6       HB
>  CB      CA      CG
> /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-2  6       HG
>  CG      CB      CD
> /usr/local/gromacs/share/gromacs/top/ffamber99sb.hdb-ASP        3
> 
> /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad:[ GLU ]
> /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad- [ atoms ]
> /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad-     N
> amber99sb_34  -0.51630     1
> /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad-     H
> amber99sb_17   0.29360     2
> /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad-    CA
> amber99sb_11   0.03970     3
> /usr/local/gromacs/share/gromacs/top/ffamber99sb.rtp.bad-    HA
> amber99sb_19   0.11050     4
> 
> 
> On Mon, Nov 9, 2009 at 4:26 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>> Jack Shultz wrote:
>>> I tried to protonate my pdb file using openbabel
>>> babel -ipdb fzd8min_renum_SS.pdb -opdb Protein.pdb -h
>>>
>>> Then I ran pdb2gmx with the following
>>>
>>> pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p
>>> Protein.top -water spce -ignh
>>>
>>> But apparently I am missing a H from my first residue. Is there an
>>> easy way to add missing atoms?
>> Yep - you may need a well-formatted .hdb file, like the message says :-) You
>> should check out whether the AMBER port you installed supports this feature
>> or not. Alternatively, have a look in the file and with a viewer to see what
>> is present for residue 1 and how the atoms are named, and whether renaming
>> some atoms will fix the issue.
>>
>> Mark
>>
>>> WARNING: atom H is missing in residue GLU 1 in the pdb file
>>>         You might need to add atom H to the hydrogen database of residue
>>> GLU
>>>         in the file ff???.hdb (see the manual)
>>>
>>>
>>> -------------------------------------------------------
>>> Program pdb2gmx, VERSION 4.0.5
>>> Source code file: pdb2top.c, line: 704
>>>
>>> Fatal error:
>>> There were 1 missing atoms in molecule Protein, if you want to use
>>> this incomplete topology anyhow, use the option -missing
>>> -------------------------------------------------------
>>>
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> 
> 
>