[gmx-users] atom H is missing in the first residue in a chain
Zhong Zheng
zhozheng at gmail.com
Thu Jan 15 08:27:07 CET 2009
Thanks Justin. I fixed it this time. I basically renamed the terminal
residues. The reason it didn't work last time is probably because some
format problem. Thanks again.
On Jan 14, 2009, at 2:50 PM, Justin A. Lemkul wrote:
>
>
> 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>
>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>> _______________________________________________
>>>>>>>>>> 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
>>>>>
>>>>> ========================================
>>>>> _______________________________________________
>>>>> 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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