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

[Yang Ye]

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,
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>           
>> __________________________________________________
>>     
>>>>> Do You Yahoo!?
>>>>> Tired of spam?  Yahoo! Mail has the best spam
>>>>>       
>>>>>           
>>>> protection around 
>>>>     
>>>>         
>>>>> http://mail.yahoo.com 
>>>>> _______________________________________________
>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>>
>>>>>           
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>     
>>>>> 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
>>>>     
>>>>         
>>>>>   
>>>>>       
>>>>>           
>>>> _______________________________________________
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>> 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
>>>>
>>>>     
>>>>         
>>> __________________________________________________
>>> Do You Yahoo!?
>>> Tired of spam?  Yahoo! Mail has the best spam
>>>       
>> protection around 
>>     
>>> http://mail.yahoo.com 
>>> _______________________________________________
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> 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
>>     
>>>   
>>>       
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> 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
>>
>>     
>
>
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection around 
> http://mail.yahoo.com 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 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
>
>