Re: [modeller_usage] model ligand

[Modeller Caretaker <>]

Bo Yang wrote:
> I fixed the alignment as the way  you suggested. This time, modeller did 
> not complain the structure problem. It went though but stopped later. 
> Here is the error message:
> --------
> fndatmi_285W> Only      464 residues out of      463 contain atoms of 
> type  CA
> delete__442E> One or more atoms absent from MODEL:  O: 454: C: 454: N: 
> 455: CA: 455:
> omgdel__425W> Unselected all O C +N +CA dihedrals:      474
> mdtrsr__446W> A potential that relies on one protein is used, yet you 
> have at
>               least one known structure available. MDT, not library, 
> potential is used.
> iup2crm_280W> No topology library in memory or assigning a BLK residue.
>               Default CHARMM atom type assigned:  FE -->  C
>               This message is written only for the first such atom.
> add_res_442E> One or more atoms absent from MODEL:  NH1:124 O1D:491
>  
> ---------
>  
> I do not quite understand the error message. The ligand in the structure 
> template is "heme". I am not sure if this is the problem. The atom 
> restrains in my .py is based on the residue ID in the template. 
> "NH1:124" is a Arg 124 in the template, "O1D: 491" is the heme ligand. I 
> don't know which part is wrong. Why the modeller says that "one or more 
> atoms absent from MODEL"?

Atom and residue numbers and names in Modeller always refer to the 
target model, not the template. This is because template PDBs can have 
inconsistent numbering, there may be multiple templates for some parts 
of the sequence, and some model residues may not be aligned to any 
templates. You can view the initial model (.ini file) to see the 
numbering Modeller is using for the model.

	Ben Webb, Modeller Caretaker
--
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