[Chimera-users] Failure Running ANTECHAMER

[Eric Pettersen]

To supplement Elaine's answer, Chimera itself will sometimes protonate an unusual structure incorrectly or make an incorrect estimate of the formal charge.  That's what happened here, which results in Antechamber's complaint about an odd number of electrons.  You would need to correct the protonation or charge estimate "by hand".  However, actually finding which compound is the problematic one is still an issue.  I don't have any better suggestions for that than what Elaine provided.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Dec 4, 2020, at 12:34 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi  Eric,
> There are occasionally specific compounds that the Antechamber method and/or AM1-BCC just can't handle, e.g. with conjugated bond patterns that are hard to discern the correct hybridization or bond order, elements not often found in organic compounds, or high charge density like polyphosphates.  On those specific compounds (you would have to figure out which ones exactly are failing) you may need to fall back to the simpler Gasteiger charge method, or if that also fails, find some other way to parametrize them. 
> 
> Normally you would tell by residue name, but I'm guessing all of your residues have the same name, ZIN.  In that case, no idea other than something really tedious like counting the number of times Antechamber was called in the Log.
> 
> Maybe an alternative (also ugly) is to make your script do the ligands one by one, writing separate mol2 files for each, and then you could see how many you got before the error.
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Dec 3, 2020, at 10:23 PM, Eric Choi <e.choi0309 at gmail.com> wrote:
>> 
>> To whom it may concern,
>> 
>> My name is Eric Choi and I am currently a student at Ithaca College doing research about virtual ligand screening where I utilize programs like Chimera and Dock6. 
>> 
>> In my workflow, I use Chimera to prepare ligands (downloaded from the ZINC database) by adding hydrogens (using the "steric only" method and "unspecified") and adding charges (AM1-BCC). Then, I run the Dock6 program, which predicts potential binding geometries and interactions of a molecule to a target protein. When I add hydrogens and charges to individual ligands (downloaded from the ZINC database), it works fine. However, when I downloaded different subsets of molecules (containing 100 ligands to 2000 ligands), an error message popped up saying that ANTECHAMBER failed to run (please see screenshots below). What does this mean? Is there any way that I can fix this issue? If a certain ligand is causing this problem, is there a way to see which one it is?
>> 
>> Thank you very much for your time and help.
>> 
>> Sincerely,
>> Eric Choi
>> 
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