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@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@cgl.ucsf.edu> Enviado el: martes, 18 de diciembre de 2018 18:56 Para: Gonzalez Fernandez, Cristina <cristina.gonzalezfdez@unican.es> CC: chimera-users@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@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.