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

Justin A. Lemkul jalemkul at vt.edu
Wed Jan 14 20:50:44 CET 2009 


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

Yes, you would have to rename all N-terminal ALA as NALA, as well as specify the 
correct Amber residue names for all other amino acids in your structure (i.e., 
C-terminal residues, histidines, etc).  An easy way might be to process your 
.pdb with xLeap (now free as part of AmberTools), and use the output .pdb as 
your input into pdb2gmx.

Have you carefully followed all instructions here:

http://chemistry.csulb.edu/ffamber/#usage

Have you updated your aminoacids.dat appropriately (see above link)?

-Justin

> 
> 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
>>>>
>>>> ========================================
>>>> _______________________________________________
>>>> 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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