[gmx-users] atom H is missing in the first residue in a chain

[Justin A. Lemkul]

Zhong Zheng wrote:
> I tried this: pdb2gmx -f prot.pdb -ignh, not working
> What I am using is : pdb2gmx -f prot.pdb -missing
> 

Does the behavior occur when you process each chain separately?

Which force field are you using?  Which version of Gromacs are you using, and 
how was it compiled?  I experienced the same behavior in version 3.3.1, 
resulting from a broken Ubuntu package.

-Justin

> 
> On Jan 14, 2009, at 2:16 PM, Justin A. Lemkul wrote:
> 
>> What is your exact pdb2gmx command line?
>>
>> -Justin
>>
>> Zhong Zheng wrote:
>>> hi
>>> Thanks for your reply. I tried -ignh and it doesn't help. I 
>>> understand -missing is bad but I made sure the only missing atoms the 
>>> program complains are the first residue in each three chains.
>>> I am using a crystal structure. However the warning messages are only 
>>> for the first residue in each chain.
>>> Zhong
>>> On Jan 14, 2009, at 1:59 PM, Justin A. Lemkul wrote:
>>>>
>>>>
>>>> Zhong Zheng wrote:
>>>>> Hi all
>>>>> I am running Gromacs on a three-chain protein. The program 
>>>>> complains about "atom H is missing in residue ALA 1 in the pdb 
>>>>> file, You might need to add atom H to the hydrogen database of 
>>>>> residue ALA in the file ff???.hdb (see the manual)". It's a warning 
>>>>> message. I can use the option -missing to ignore it. However I 
>>>>> would like to understand this. It's always the first residue in the 
>>>>> chain. So I am thinking this is because they are the n-terminus. 
>>>>> Then why no complain about c-terminus? How can I fix this?
>>>>
>>>> Use -ignh to allow the relevant .hdb file to add the appropriate 
>>>> hydrogens.  The problem is that, without -ignh, pdb2gmx expects all 
>>>> atoms (including H) to be present in the .pdb file.  If you are 
>>>> using a crystal structure, this requirement will not be satisfied.
>>>>
>>>> Likely pdb2gmx does not complain about the C-terminus because it is 
>>>> unprotonated, or otherwise the program exits after finding a missing 
>>>> N-terminal hydrogen.
>>>>
>>>> As an aside, using -missing is generally a very bad idea, unless you 
>>>> have a very specific (and anticipated!) reason to use it.
>>>>
>>>> -Justin
>>>>
>>>>> Thanks a lot.
>>>>> Zhong Zheng
>>>>> Ph.D candidate
>>>>> Physics Dept., City College-CUNY
>>>>> Marshak Science Building J-419 , 160 Convent Ave, New York, NY 
>>>>> 10031 USA
>>>>> Tel: (212)650-6079 MCCE wiki: scratchpad.wikia.com/wiki/MCCE 
>>>>> <http://scratchpad.wikia.com/wiki/MCCE>
>>>>> ------------------------------------------------------------------------ 
>>>>>
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>>>>
>>>> -- 
>>>> ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Graduate Research Assistant
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>>> ========================================
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>>
>> -- 
>> ========================================
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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> 
> 

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================