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

[Justin A. Lemkul]

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

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