FAQs
For questions not addressed by a support solution here, please Contact Us. Please do include a description of the problem as well as your operating system and version.
What can we help you with?
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Which file formats does GOLD support?
… Acceptable input and output ligand file formats are: mol2 (i.e. Tripos format)Of the possible ligand input formats, only mol2 can be used if you wish to set …
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What should I input to Mogul?
… In general you should input complete molecules, ions or crystal structures to Mogul rather than substructures. The geometrical preferences of a bond length …
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Mercury will not read my CIF input file. What am I doing wrong?
… Mercury expects certain information to be present within an input file - if certain key data are not present, then Mercury may fail to read in the file.In …
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What input file format do I need for a Hydrogen Bond Propensity calculation?
… The Hydrogen Bond Propensity tool (accessed from within Mercury) accepts molecular input in a wide variety of formats. If you simply want to assess …
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Can I search on CSD refcodes within ConQuest?
… Refcode into the input box.It is also possible to search for all occurrences of a particular refcode, for example, to retrieve all structures where the first …
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Can GOLD handle metals?
… protein atoms or water molecules in the original file so that GOLD can predict the coordination geometry. When the protein input file is prepared, the metal ion …
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GOLD fails to recognise the metal in my metal-containing enzyme
… type## > > Setting atom ##### to type Du A possible work-around is to re-type the metal atom in the protein input file to one of the included metal atom types …
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Is it possible to re-score a given set of GOLD solutions using an alternative scoring function?
… , requires a prepared protein input file and a fully defined binding site (preferably the same definition that was used for the original docking). The ligand(s …
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Why do I get different fitness scores for consecutive dockings with the same input files?
… Consecutive dockings using the same input files will not give identical solutions or fitness scores. The reason for this is fundamental to the way in which …
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How can I view only the ligand and surrounding residues rather than the whole protein-ligand complex?
… to 'Selection', then 'Select', then 'Set Selection Radius', then input a value e.g. 10 for creating a 10 Angstroms selection around your ligand. To select all atoms …
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