[Chimera-users] Non-standard atom names

[Elaine Meng]

Hi Sid,
To understand these things yourself, you need to look at what specific atoms are mentioned in the Log, and then look at them in the structure.    Also it would be useful if you said more about what steps you did, because we do not have the resources to consult on everybody’s research project in detail.

To test, I assumed you are only using chain A of 2Y9W so I deleted everything else.  I also deleted all the known “nonstandard” residues in that chain except CU  (look in menu: Select… Residues  for list of nonstandard residues in open structures).  Then I saved PDB for a later step, see below.

open 2y9w
delete ~ :.a
delete :ho,hoh,peg
write 0 ~/Desktop/2y9wA.pdb

Then I tried running Dock Prep because it will also fix partially missing residues before it tries to add hydrogens and charges (I turned off the “write Mol2” choice but left everything else default).  Then I ran got the message about non-integral charges in residue His 85.  That is how you know what part of the structure to look at carefully.  In the structure, I see that His 85 is not really standard but instead covalently bonded to Cys 83.  So problems could be caused by these two residues having standard names when they are not really standard.

So next I re-open the saved PDB file and change 85 to HXX and 83 to CXX.

setattr r type HXX :85
setattr r type CXX :83

Then I use Dock Prep again with defaults (except turned off “write Mol2”) and then when I get to the charge dialog, chose Gasteiger method because it’s faster for testing and used the guess of -1 for CXX+HXX

Then everything runs OK, net charge is integral.

In the future, now you know how to investigate and fix similar problems!  I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On May 8, 2019, at 3:46 AM, Sid Majaha <sidumomajaha at live.com> wrote:
> 
> Hello. I am using the tyrosinase protein, 2Y9W for docking but I am having some difficulties using chimera. I want to prepare docking by adding hydrogen and charges but its giving me an error message of
> ‘Correct charges are unknown for 2 non-standard atom names in otherwise standard residues.
>  
> Charges of 0.0 were assigned to the unknown atoms’
>  
> In my protein< I did not remove two copper ions because my ligand will have to the two copper atoms after docking.
> Please help me add the charges to my receptor.
>  
> Thank you Sid
>