[gmx-users] Converting SDF to Mol2 Format

Nancy nancy5villa at gmail.com
Fri Mar 26 18:47:47 CET 2010

Hello All,

I need to convert a large number of PubChem SDF files into Mol2 format, for
input into Gromacs.  I have been using UCSF Chimera to convert an SDF file
into Mol2 format; I use Chimera to add partial charges and run energy
minimisation on the molecule.  So far, I have only been able to convert
individual files using this method.  Is there another way to convert a large
number of SDF files to Mol2 format at once, and also preserve the filenames?

Thanks in advance,

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