Hi list,
We're in the process of developing Avogadro 2, and I'm currently adding an
interface to perform the obabel minimize operation on a molecule.
My question: Is there a heuristic that can be used to select the best
forcefield for a given molecule? As I understand it:
* Ghemical is good for
On 2013-02-04 16:24, David Lonie wrote:
Hi list,
We're in the process of developing Avogadro 2, and I'm currently adding
an interface to perform the obabel minimize operation on a molecule.
My question: Is there a heuristic that can be used to select the best
forcefield for a given
* Are there cases where MMFF94s should be preferred to Ghemical?
Everything. The heuristic should be something like MMFF94 if it works, UFF
otherwise. Ghemical is included for backwards-compatibility -- it was much
easier to implement than MMFF94.
* Is GAFF particularly good at any systems
On 2013-02-04 17:18, Geoffrey Hutchison wrote:
* Are there cases where MMFF94s should be preferred to Ghemical?
Everything. The heuristic should be something like MMFF94 if it works, UFF
otherwise. Ghemical is included for backwards-compatibility -- it was much
easier to implement than
On Mon, Feb 4, 2013 at 11:22 AM, David van der Spoel sp...@xray.bmc.uu.se
wrote:
On 2013-02-04 17:18, Geoffrey Hutchison wrote:
* Are there cases where MMFF94s should be preferred to Ghemical?
Everything. The heuristic should be something like MMFF94 if it works,
UFF otherwise. Ghemical is
Speed? Should make no difference at all. Lennard Jones + Coulomb on
point charges. It is rather not for proteins (that is regular Amber) but
for small (organic) ligand molecules.
I stand corrected. I should point out that David really does this for a living.
In comparison, I just pretend.
I'll take a look at the sources and see if I can figure out when they'll
fail, and use GAFF-MMFF94-UFF.
Thanks for the feedback!
Dave
On Mon, Feb 4, 2013 at 1:22 PM, Geoffrey Hutchison
geoff.hutchi...@gmail.com wrote:
Speed? Should make no difference at all. Lennard Jones + Coulomb on
