[Chimera-users] Topology error

[Elaine Meng]

Dear Cristina,
You cannot use the Autodock Vina web service connected to that tool with that large a ligand, sorry.

The way to solve it is more work for you:  download Autodock Vina to your computer and use it directly, 
<http://vina.scripps.edu/>

...or find some other website/webservice that allows docking such a large ligand.  I don’t know any specifically, but I haven’t looked.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Dec 18, 2018, at 11:43 PM, Gonzalez Fernandez, Cristina <cristina.gonzalezfdez at unican.es> wrote:
> 
> 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,
> C.
> 
> -----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:
> 
> <http://www.swissdock.ch/docking>
> 
> 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
> -----
> 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.