[gmx-users] Error when adding a unnatural amio acid

Yang Ye leafyoung81-group at yahoo.com
Wed Jan 3 22:14:32 CET 2007


To debug this problem. I suggest you to create a pdb file which contains 
only ASO residue and play with pdb2gmx.

Regards,
Yang Ye

On 1/4/2007 1:26 AM, yuemin liu wrote:
> It does not work either. Thanks anyway. I doubt the
> error results from sth else. Most likely the reason is
> default angle and dihedral values in the modified
> ffgmxbon.itp file. By the way, how would you assign
> default angle and dihedral values? Structurally it is
> fine unless the size matters, because the new amino
> acid has almost 200 atoms.
>
> Best wishes,
>
> --- Yang Ye <leafyoung81-group at yahoo.com> wrote:
>
>   
>> Hi,
>>
>> You may try Dr Mu's suggestion:
>> check file xlateat.dat and find any line matching
>>     protein XXX H1
>>
>> XXX could be any name of an atom. Remove this line
>> and decrement the 
>> number on the top.
>>
>> Regards,
>> Yang Ye
>>
>> On 1/3/2007 11:18 PM, yuemin liu wrote:
>>     
>>> I did add the resname in aminoacids.dat and also
>>> change the the number on the top. It still
>>>       
>> complains
>>     
>>> same thing. It is H atom type also name H
>>>       
>> (connecting
>>     
>>> to N) in the new amino acid like the regular amino
>>> acid, and has nothing to do with H1 at all.
>>>
>>> Thanks,
>>>
>>> Liu, Yuemin
>>>  
>>> --- Yang Ye <leafyoung81-group at yahoo.com> wrote:
>>>
>>>   
>>>       
>>>> You may try add residue name ASO to the end of
>>>> /top/aminoacids.dat and 
>>>> also increment the number on the top.
>>>>
>>>> Regards,
>>>> Yang Ye
>>>>
>>>> On 1/3/2007 8:55 AM, yuemin liu wrote:
>>>>     
>>>>         
>>>>> Hi, Everyone,
>>>>>
>>>>> I got Error when adding a unnatural amio acid in
>>>>>           
>> a
>>     
>>>>> protein. I have all the rtp and hdb file
>>>>>           
>> modified
>>     
>>>>> using information either from ffgmx.rtp
>>>>>           
>> ffgmx.hdb
>>     
>>>>>       
>>>>>           
>>>> or
>>>>     
>>>>         
>>>>> thr rtp file form progdrg. There is no H1 in
>>>>>       
>>>>>           
>>>> either
>>>>     
>>>>         
>>>>> rtp file or my new pdb file. When I try use
>>>>>       
>>>>>           
>>>> pdb2gmx to
>>>>     
>>>>         
>>>>> generate top file, it always give the error
>>>>>       
>>>>>           
>>>> message
>>>>     
>>>>         
>>>>> following;
>>>>> "Atom H1 not found in rtp database in residue
>>>>>           
>> ASO,
>>     
>>>>>       
>>>>>           
>>>> it
>>>>     
>>>>         
>>>>> looks a bit like H". I know it refers to the
>>>>>       
>>>>>           
>>>> Hydrogen
>>>>     
>>>>         
>>>>> of the peptide bond which has nothing wrong
>>>>>           
>> there.
>>     
>>>>> Hope can get help from you with this,
>>>>>
>>>>> Thanks,
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>           
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