Thank you Dr Case
On Wed, Jul 27, 2011 at 8:57 AM, case <case.biomaps.rutgers.edu> wrote:
> 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 - 08:30:04 PDT
