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

[yuemin liu]

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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