[gmx-users] pdb2gmx -missing

[Tsjerk Wassenaar]

Hi,

Well, -ignh is not the right answer here. I recall that just a few
days ago someone posted the same problem. For Amber you need to tag
the first and last residue. For your GLY, it means you have to rename
it to NGLY.

Itamar,

The warning mentions an atom missing from the .pdb file. These have to
be built according to the rules in the .hdb file. The option -ignh is
to strip off hydrogen atoms that are present in the .pdb file, but are
not listed in the .rtp file and are thus not part of the residue
according to the force field. Please make sure that your replies are
to the point, because replies that are amiss may confuse the original
poster and bring them even further from solving their problems.

Cheers,

Tsjerk

On Wed, Nov 11, 2009 at 9:16 AM, Itamar Kass <itamar.kass at gmail.com> wrote:
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist