[gmx-users] pdb2gmx -missing

[Itamar Kass]

Hi,

Try to use -ignh.

On Wed, Nov 11, 2009 at 7:09 PM, leila karami <karami.leila1 at gmail.com> wrote:
> I do command pdb2gmx but follow warning and error is came up:
>
> WARNING: atom H is missing in residue GLY 1 in the pdb file
>          You might need to add atom H to the hydrogen database of residue
> GLY
>          in the file ff???.hdb (see the manual)
>
> Fatal error:
> There were 1 missing atoms in molecule Protein_A, if you want to use this
> incomplete topology anyhow, use the option -missing
>
> my pdb file is:
>
> HETATM    1  N   GLY A   1      19.949  29.046  10.462
> HETATM    2  CA  GLY A   1      19.485  28.078   9.486
> HETATM    3  C   GLY A   1      20.152  28.247   8.136
> HETATM    4  O   GLY A   1      19.859  29.193   7.405
> HETATM    5 1H   GLY A   1      20.545  29.773  10.181
> HETATM    6 2HA  GLY A   1      19.690  27.084   9.856
> HETATM    7 2H   GLY A   1      20.356  28.562  11.250
> HETATM    8 3H   GLY A   1      19.099  29.546  10.681
> HETATM    9 1HA  GLY A   1      18.415  28.236   9.347
>
> and my ffamber03.hdb of gly is
>
> GLY 2
> 1 1 H N -C CA
> 2 6 HA CA N C
>
> NGLY 2
> 3 4 H N CA C
> 2 6 HA CA N C
>
> how I add H to hdb file?
>
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