[gmx-users] pdb2gmx -missing

[Itamar Kass]

Sorry if I made someone more confuse, I thought this was the problem.
Probably reading the original post again would have a wise step.

Itamar

On Wed, Nov 11, 2009 at 7:25 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 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
> --
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