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

[Zhong Zheng]

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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