Re: Ficoll/Dextran CHARMM Force Field

From: Angelo Rossi (
Date: Tue Aug 23 2022 - 08:55:42 CDT


The following is one possible solution:

Step 1: Obtain a structure for these molecules. I found
Conformer3D_CID_71315856.sdf in PubChem for Dextran 70.

Step 2: Convert the sdf file to a mol2 file with OpenBabel.
obabel -iSDF Conformer3D_CID_71315856.sdf -o mol2 -O

Step 3: Use the CGenFF Program (;!!DZ3fjg!9zpjnKCijKKBiUjRECmzq2fZUlFQ3-_7LhgYtFDHa6kYxKn70zel7h7eFVqL9e5oFm-AXNHVWQo_TM5ieSWGyPwcToIH$ ) to convert
the Conformer3D_CID_71315856.mol2 file
to a Conformer3D_CID_71315856.str file.

Note the Conformer3D_CID_71315856.str file can now be concatenated with the
simulation parameters within a namd input file.

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