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.
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.
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.
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.
participants (2)
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Elaine Meng -
Gonzalez Fernandez, Cristina