[gmx-users] Missing H from residue
Jack Shultz
js at drugdiscoveryathome.com
Mon Nov 9 22:54:13 CET 2009
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.
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
/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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--
Jack
http://drugdiscoveryathome.com
http://hydrogenathome.org
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