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

[Yang Ye]

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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