[gmx-users] Missing H from residue
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Nov 10 02:38:29 CET 2009
Jack Shultz wrote:
> I modified the N-Terminal and C-Terminal Residues.
>
> [boincadm at vps test]$ grep NGLU ProteinAmber.pdb && grep CARG ProteinAmber.pdb
> ATOM 1 N NGLU 32 -20.050 8.920 -4.700 1.00 0.00
> N
> ATOM 2 CA NGLU 32 -19.847 8.507 -3.304 1.00 0.00
> C
> ATOM 3 C NGLU 32 -20.807 7.451 -2.751 1.00 0.00
> C
> ATOM 4 O NGLU 32 -21.843 7.183 -3.340 1.00 0.00
> O
> ATOM 5 CB NGLU 32 -19.913 9.782 -2.416 1.00 0.00
> C
> ATOM 6 CG NGLU 32 -18.641 10.678 -2.498 1.00 0.00
> C
> ATOM 7 CD NGLU 32 -18.573 11.627 -1.334 1.00 0.00
> C
> ATOM 8 OE1 NGLU 32 -19.009 12.797 -1.488 1.00 0.00
> O
> ATOM 9 OE2 NGLU 32 -18.089 11.174 -0.257 1.00 0.00
> O
> ATOM 10 HA NGLU 32 -18.845 8.057 -3.227 1.00 0.00
> H
> ATOM 11 HB1 NGLU 32 -20.805 10.368 -2.695 1.00 0.00
> H
> ATOM 12 HB2 NGLU 32 -20.026 9.493 -1.358 1.00 0.00
> H
> ATOM 13 HG1 NGLU 32 -17.724 10.072 -2.453 1.00 0.00
> H
> ATOM 14 HG2 NGLU 32 -18.628 11.255 -3.435 1.00 0.00
> H
> ATOM 15 HT2 NGLU 32 -19.381 9.526 -5.140 1.00 0.00
> H
> ATOM 16 HT1 NGLU 32 -20.892 8.644 -5.172 1.00 0.00
> H
> ATOM 3819 N CARG 153 -2.889 -18.736 0.849 1.00 0.00
> N
> ATOM 3820 CA CARG 153 -4.210 -19.301 1.173 1.00 0.00
> C
> ATOM 3821 C CARG 153 -4.155 -20.743 1.653 1.00 0.00
> C
> ATOM 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00
> O
> ATOM 3823 CB CARG 153 -5.123 -19.172 -0.074 1.00 0.00
> C
> ATOM 3824 CG CARG 153 -5.347 -17.677 -0.414 1.00 0.00
> C
> ATOM 3825 CD CARG 153 -6.074 -17.485 -1.764 1.00 0.00
> C
> ATOM 3826 NE CARG 153 -7.488 -17.868 -1.625 1.00 0.00
> N
> ATOM 3827 CZ CARG 153 -8.038 -19.003 -1.986 1.00 0.00
> C
> ATOM 3828 NH1 CARG 153 -7.368 -20.017 -2.446 1.00 0.00
> N
> ATOM 3829 NH2 CARG 153 -9.327 -19.146 -1.882 1.00 0.00
> N
> ATOM 3830 HA CARG 153 -4.670 -18.715 1.987 1.00 0.00
> H
> ATOM 3831 OXT CARG 153 -3.778 -21.646 0.751 1.00 0.00
> O
> ATOM 3832 HT CARG 153 -3.770 -22.506 1.154 1.00 0.00
> H
> ATOM 3833 HB1 CARG 153 -4.628 -19.690 -0.911 1.00 0.00
> H
> ATOM 3834 HB2 CARG 153 -6.096 -19.657 0.114 1.00 0.00
> H
> ATOM 3835 HG1 CARG 153 -5.942 -17.224 0.393 1.00 0.00
> H
> ATOM 3836 HG2 CARG 153 -4.393 -17.125 -0.460 1.00 0.00
> H
> ATOM 3837 HD1 CARG 153 -6.049 -16.397 -1.960 1.00 0.00
> H
> ATOM 3838 HD2 CARG 153 -5.519 -17.914 -2.612 1.00 0.00
> H
> ATOM 3839 HE CARG 153 -8.133 -17.122 -1.290 1.00 0.00
> H
> ATOM 3840 1HH1 CARG 153 -7.834 -20.881 -2.736 1.00 0.00
> H
> ATOM 3841 2HH1 CARG 153 -6.359 -19.962 -2.559 1.00 0.00
> H
> ATOM 3842 1HH2 CARG 153 -9.802 -20.000 -2.173 1.00 0.00
> H
> ATOM 3843 2HH2 CARG 153 -9.904 -18.331 -1.627 1.00 0.00
> H
> ATOM 3844 HN CARG 153 -2.612 -18.555 -0.097 1.00 0.00
> H
> TER 3845 CARG 153
>
> This time I did not protonate with babel
>
> pdb2gmx -ff amber99sb -f ProteinAmber.pdb -ignh
>
> Back Off! I just backed up topol.top to ./#topol.top.6#
> Processing chain 1 (1976 atoms, 244 residues)
> There are 362 donors and 364 acceptors
> There are 561 hydrogen bonds
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.0.5
> Source code file: pdb2gmx.c, line: 429
>
> Fatal error:
> Atom O in residue CARG 244 not found in rtp entry with 25 atoms
> while sorting atoms
> -------------------------------------------------------
>
> But we got an O here
> ATOM 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00 O
Yes, but the residue number doesn't make sense. Since you have 153+1 -
32 = 122 residues and pdb2gmx doesn't like number 244, I guess that you
have two structures in your .pdb file. If so, I posted some coping
strategies in the last week or two for this case. Telling us what (you
think) is in your structure file would have been a good idea :-)
Mark
> On Mon, Nov 9, 2009 at 6:54 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>> 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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>>>
>>>
>> --
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