[Chimera-users] Topology error

Gonzalez Fernandez, Cristina cristina.gonzalezfdez at unican.es
Tue Dec 18 23:43:07 PST 2018

Dear Elaine,

You are right, the problem is the size of my ligand, because I have also tried with the Autodock Vina of Chimera and I get this error: "Too many heavy atoms (>100)". Do you know how I can solve it?. My ligand is a lipid, so its bigger than common ligands, but much smaller than my protein.

I attach the pdb file of my ligand.

Thank you very much,

-----Mensaje original-----
De: Elaine Meng <meng at cgl.ucsf.edu> 
Enviado el: martes, 18 de diciembre de 2018 18:56
Para: Gonzalez Fernandez, Cristina <cristina.gonzalezfdez at unican.es>
CC: chimera-users at cgl.ucsf.edu
Asunto: Re: [Chimera-users] Topology error

Dear Cristina,
You should probably ask the SwissDock people, since we don’t know the details of what their server requires.  I’m guessing you are using this website:


Also they probably wouldn’t be able to tell you anything either unless you include the file you were trying to upload. The ligand should probably be a small molecule and not contain metals or rare elements, but that’s just my guess.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Dec 18, 2018, at 1:43 AM, Gonzalez Fernandez, Cristina <cristina.gonzalezfdez at unican.es> wrote:
> Dear Chimera users,
> I want to perform molecular docking by using Swiss Dock. Therefore, I have used Chimera to remove the molecules that I don’t want from the PDB file, add hydrogens and save as mol2. However, when I tried to upload the mol2 file in SwissDock I get this error:  “Ligand setup failed. Please check that your structure file has a correct topology. No extra info available”.
> Does anyone know what I am doing wrong?
> Thank you in advance,
> C.

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