I wanted to follow up on a previous post in which I asked about how to save molecules in mol2 format for submission to the paramchem.org for automated atom typing and parameter assignment for the cgenFF.

This was very straightforward using Accelerys' Discovery Studio 2.5 (a successor to their Insight II software, I believe, so I imagine this should be similarly straightforward using that program as well).

Here are the steps I followed, after opening Discovery Studio. (I suspect that, e.g., existing files in non-pdb formats would work well too, but I haven't tried.)

1. Open pdb file of molecule of interest. (Mine was a pdb, previously edited for charmm use, of just my ligand of interest.)

2. Adjust charge states if necessary. (To find out charges, select Structure --> Labels --> Add, and then choose Object --> Atom / Attribute --> Formal Charge / --> OK. To adjust charge, select Chemistry --> Charge --> {+1 or -1 or Set}.)

3. Check hybridization states of molecule's atoms.

4. Add hydrogens. Chemistry --> Hydrogens --> Add

5. Check that an appropriate number of hydrogens were added to each atom.

6. Choose "Save As..." from the File menu.

7. Select "Sybyl MOL2 Files (*.mol2)" from the "Files of Type" drop-down menu, under the filename input box.

8. Choose appropriate name and directory for saving.

This produced a file with correct SYBYL atom types. Submission to paramchem was successful.

NOTE: It appears that the charge of a heteroatom can be altered after hydrogens are added, and an appropriate adjustment in the number of hydrogens will be made automatically.

Intestinal nematode
Bronx, NY