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

[Zhong Zheng]

You mean rename ALA as NALA in the .pdb for the n-terminus Ala? If so,  
i tried already and still not working.


On Jan 14, 2009, at 2:38 PM, Justin A. Lemkul wrote:

>
> Please keep all correspondence on the list.
>
> Zhong Zheng wrote:
>> Yes.
>> Amber. Gromacs Version 4.0.2. It's compiled on my computer,  
>> macbook. I followed standard procedure,nothing special.
>
> The Amber force fields use their own special nomenclature, so N- 
> terminal alanine would actually be called NALA.  You will have to  
> modify your .pdb file to correspond with Amber naming conventions  
> before this step will complete properly.
>
> -Justin
>
>> On Jan 14, 2009, at 2:28 PM, Justin A. Lemkul wrote:
>>>
>>>
>>> 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
>>>>>>>
>>>>>>> ========================================
>>>>>>> _______________________________________________
>>>>>>> gmx-users mailing list    gmx-users at gromacs.org
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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
>>>>>
>>>>> ========================================
>>>>> _______________________________________________
>>>>> gmx-users mailing list    gmx-users at gromacs.org
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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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