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

Wed Jan 14 20:38:08 CET 2009

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
>>>>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>>>>> Please search the archive at http://www.gromacs.org/search before 
>>>>>>> posting!
>>>>>>> Please don't post (un)subscribe requests to the list. Use the www 
>>>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>>
>>>>>> -- 
>>>>>> ========================================
>>>>>>
>>>>>> 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
>>>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>>>> Please search the archive at http://www.gromacs.org/search before 
>>>>>> posting!
>>>>>> Please don't post (un)subscribe requests to the list. Use the www 
>>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>
>>>> -- 
>>>> ========================================
>>>>
>>>> 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
>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at http://www.gromacs.org/search before 
>>>> posting!
>>>> Please don't post (un)subscribe requests to the list. Use the www 
>>>> interface or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>> -- 
>> ========================================
>>
>> 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
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before 
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www 
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 

-- 
========================================

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

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