[Chimera-users] Converting SDF files to Mol2 Format

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 29 14:44:30 PDT 2010

On Mar 29, 2010, at 12:48 PM, Eric Pettersen wrote:

> 	A final possibility is to use the PubChem3D (<http://pubchem.ncbi.nlm.nih.gov/release3d.html 
> >) files and convert them directly to Mol2 files.  This would  
> require the 1.5 release (the 1.4 series doesn't read the charges in  
> the SDF file) and assumes that the included MMFF charges are  
> sufficient for your needs and that the conformer provided is good  
> enough for your purposes without minimization.

Just a short note regarding PubChem3D... as discussed previously,


you may not want to use their charges because functional groups such  
as amines and acids are in their neutral forms rather then the charged  
ones more likely at physiological pH.

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