Hello, I used E-Dragon to calculate the molecular descriptors, but when I used some SMILES of chemicals, it showed errors, for example, I succeeded to get the molecular descriptor data of O=[Cr](=O)=O, but I couldn't get the data for O=S1(=O)O{-}.[Fe]{2+}.O{-}1 or Cl{-}.[Cd]{2+}.Cl{-}. Does anyone also use E-Dragon or Dragon, do you know why I had this kind of problem?
Try connecting to http://146.107.217.178/lab/edragon/start.html then click on edit data and paste your SMILES, be sure to set the correct file format to SMILES (there is a drop down list to select the proper file format) and convert to 3D using CORINA, there is a drop down list on the rights side of the java applet that enables you to select the proper engine to convert a SMILES to a 3D form. Then submit your task. It works properly with your SMILES.
Prepare your molecules in MOL2 (Sybyl) file format and you calculate properties in E-Dragon
E-Dragon accepts SMILES as input file format. You can directly use CORINA to convert 2D SMILES structures to 3D molecular strucures.
You can always inspect the dragon.log ('Result as text' menu). dragon.log reports warnings and errors occured during calculation.
The O=S1(=O)O{-}.[Fe]{2+}.O{-}1 or Cl{-}.[Cd]{2+}.Cl{-} SMILES has several problems:
- it is not a standard SMILES: {and } are not allowed in standard SMILES, charged atoms should be reported as [Fe2+] and not as [Fe]{2+} (see daylights SMILES tutorial );
- it is a disconnected structure. Disconnected structures are not allowed.
Hello, I try to use e-dragon but it does not converte my SMILES by CORINA. For example : tramadol CN(C)C[C@H]1CCCC[C@@]1(c2cccc(c2)OC)O was not converted. I used Chem spider to obtain my SMILES.
have you an idea about how to solve this problem?
Thx
Try connecting to http://146.107.217.178/lab/edragon/start.html then click on edit data and paste your SMILES, be sure to set the correct file format to SMILES (there is a drop down list to select the proper file format) and convert to 3D using CORINA, there is a drop down list on the rights side of the java applet that enables you to select the proper engine to convert a SMILES to a 3D form. Then submit your task. It works properly with your SMILES.
Thx For you answer. I have just do as you advised. Here is the result (when pressing on inspect WARNING)
Conversion problems: only 1 out of 58 molecules were converted. Check (format of) your data.
mol #2 "GLcorina" was not converted
mol #3 "CORINA" was not converted
mol #4 "11" was not converted
mol #5 "-0.0187" was not converted
mol #6 "0.0021" was not converted
mol #7 "-1.4333" was not converted
mol #8 "1.0039" was not converted
mol #9 "-0.5459" was not converted
mol #10 "-0.5289" was not converted
Since only 1 out of 10 first molecules were successfully converted, the further conversion was stopped.
You are doing it wrong. The warning messages you got are due to the fact that the molecules you are trying to convert to 3d using CORINA are not SMILES but the sample default molecule provided by e-dragon applet (MDL file format). In order to calculate molecular descriptors using e-dragon you have to load your molecules. You can do it in two ways:
1. click on the link on: "click to see or edit data" and paste your SMILES in the pop-up window;
2. click on "upload data" button, a pop-up menu appears and then load your file.
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