creating a Mol2 file with charges assigned to atoms

Is it possible to obtain a mol2 file with atoms having charges assigned in Marvin?

Yes, it is possible. Select the "Tripos Mol2 files" file type when you save the file, or in the source window (Edit | Source) select the "Tripos Mol2" format. As an example, I created the attached file (with Marvin Sketch 4.1.8).

We can select tripos mol2 as an option, but still dont get the charges out.


We therefore are making a mistake earlier in the process.


Our steps are:


1. Construct molecule in 2D


2. Convert to 3D using Clean 3D optimize


3. Tools charge (this opens a new window with the charges displayed; this window is not editable)


4. Return to main save as tripos mol2 (we also try edit, source, format, tripos mol 2)


5. Either way we get coordinates but no charges.

Unfortunately, Marvin presently does not support saving the partial charges into mol2 format, and I cannot promise it will do in the near future. On the other hand, I will create this future request in our task list, and as soon as we have an exact plan for the implementation we will inform you. Until that, you might use different file formats for storing the calculated charges (although only as atom values), like mrv or mol.