On Tue, Jul 26, 2011, David Cantu wrote:
>
> I am preparing a substrate. I optimized the structure with Gamess, and
> converted the Gamess output into a mol2 file using OBabel. The mol2 file has
> SYBYL atom types after the xyz coordinates. I now need antechamber to read
> this, and convert it to Gaff atom types.
>
> I tried:
>
> antechamber -i file.mol2 -if mol2 -o file-1.mol2 -fo mol2
> And it did convert to Gaff types, but the bond types were not kept!
Amber never uses the bond types in any energy calculation. If you ask
antechamber for gaff atom types, it automatically estimates "gaff bond types"
as well; these can be useful in understanding how antechamber determines atom
types, but not for much else.
>
> I can go in and manually edit the file,
Sounds like a plan, if you need some other bond types than the ones that
antechamber assigns.
> Or, can I load the mol2 with SYBYL atom types directly into Xleap with GAFF?
Technically, you could load a mol2 file with sybyl types into LEaP, but you
couldn't create a prmtop file from them, since the required parameters are not
available.
....dac
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Received on Wed Jul 27 2011 - 07:00:02 PDT
