AutoDock-Vina
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ccsb-scripps
AutoDock Vina
I prepared a PDB file with a structure of beta-cyclodextrin (BCD.pdb), based on crystallographic data. Beta-cyclodextrin is a cyclic macromolecule, consisting of seven linked glucose residues. I would like to...
Hi @diogomart, I'm trying to optimize Vina parameters to get better agreement with experiment for docked binding energies of small molecules to cyclodextrins. To do this, I'd like to be...
File like mode | affinity | dist from best mode | (kcal/mol) | rmsd l.b.| rmsd u.b. -----+------------+----------+---------- because it appears in my terminal only i want this as extra...
During Vina flexible docking ligands are getting break .I have used vina_split command to split binding poses .I am attaching screenshots of same for your reference, can you help for...
Hello, I have been trying to set up some docking analyses using the AutoDock4Zn protocol, but the receptor I am working on has a rarer conformation type (with an adjacent...
Hello, I was wondering if I can use AutoDock-Vina for docking between proteins and peptides.If not, do you have other suggestions? Best Regards Soodabeh
Hello, I want to perform flexible docking. However, when I run `vina`, the job doesn't proceed. No error is raised. I checked the rigid and flexible parts of the receptor,...
ERROR: Affinity map for atom type P is not present. ERROR: Affinity map for atom type F is not present. ERROR: Affinity map for atom type Cl is not present.
Hi All, My protein contains a Ni metal. I thought the parameter file was the parameter files in AutoDock-Vina/data AD4Zn.dat vs AD4_parameters.dat so i put Ni into those files. However,...
I have tried with 5 lignads(such as 5wl0,1jla,1aet,5tim,4fev) for Vina GPU with the center values and box volume(x,y,x) which worked fine while in Autodock Vina CPU(for 1.2.5) with corrosponding value...
