[Chimera-users] No MMTK name for atom "H" in standard residue "GLY"

[Marco Sette]

Hi Eric,

it works ! :)

Thanks a lot,

Best,

Marco

Il 14/11/2022 22:24, Eric Pettersen ha scritto:
> Hi Marco,
> 	Chimera assigns partial charges and atom types to the atoms of standard residues by looking up the atom name in a table.  That means that those atoms have to have their PDB standard names.  There is no atom named 'H' in a standard N-terminal glycine.  The hydrogens attached to the N should be named H1, H2, and H3, and the ones attached to the CA should be named HA1 and HA2.
> 	Assuming it wasn't Chimera that added this 'H', an easy way to fix it is with the commands (Favorites→Command Line) "del H" followed by "addh".  Then you should be able to minimize.
>
> --Eric
>
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
>
>
>> On Nov 12, 2022, at 3:15 AM, Marco Sette via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>>
>> Dear all,
>>
>> i'm trying to minimize a peptide (Tools, Structure editing, Minimize Structure) but I obtain this error message: No MMTK name for atom "H" in standard residue "GLY".
>>
>> I have a Gly in position 1, does this depends on the NH protonation?
>>
>> Also, I fixed most of the residues, including Gly 1, trying to minimize a small region (Fixed Atoms: selected, in minimize panel) but still have the same errors.
>>
>> How can I solve it?
>>
>> Thanks for your help,
>>
>> Best
>>
>> Marco
>>
>>
>> -- 
>> Dr Marco Sette, PhD.
>> Department of Chemical Sciences and Technology
>> University of Rome, "Tor Vergata"
>> via della Ricerca Scientifica, 00133, Rome, Italy
>> e-mail: sette at uniroma2.it
>> Tel.: +39-0672594424
>>
>>
>> -- 
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-- 
Dr Marco Sette, PhD.
Department of Chemical Sciences and Technology
University of Rome, "Tor Vergata"
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail: sette at uniroma2.it
Tel.: +39-0672594424