Hi again,
I've successfully used the UFF force field to minimize an OBMol. I'm
now trying to use the Gaff, Ghemical and MMFF94 force fields, but none
will work.
Even after copying all files from the /data folder (including .prm
files) in the latest source to my executable directory, I get a list
of errors beginning like this:
COULD NOT FIND PARAMETERS FOR BOND ...
COULD NOT FIND PARAMETERS FOR TORSION ...
^ This is what happens with the Gaff and Ghemical FFs. With the
MMFF94, I get a message saying "ERROR Could not setup forcefield.".
I have read a SMILES in and (unlike earlier) am beginning with zero
positions for all atoms.
Any advice would be welcome, sorry to ask again. I haven't yet found
any further info to help me in the API documentation.
With thanks and kind regards,
David
On 1 August 2010 00:19, N David Brown <hubd...@googlemail.com> wrote:
> I didn't call that function, no. Many thanks, Tim.
>
> It might be worth exemplifying this in at least one of the examples in
> the API documentation to save others the same confusion (or maybe it's
> just me!).
>
> David
>
>
> On 1 August 2010 00:02, Tim Vandermeersch <tim.vandermeer...@gmail.com> wrote:
>> Did you call OBForceField::GetCoordinates after minimizing? The
>> forcefield works on a copy of the molecule so you have to get the
>> updated coordinates explicitly.
>>
>> On Sun, Aug 1, 2010 at 12:44 AM, N David Brown <hubd...@googlemail.com>
>> wrote:
>>> ..whoops, that's FOR_ATOMS_OF_MOL of course, just a typo (!).
>>>
>>>
>>> On 31 July 2010 23:43, N David Brown <hubd...@googlemail.com> wrote:
>>>> Hi all,
>>>>
>>>> I'm having issues with OBForceField.
>>>>
>>>> I perform a crude layout of a SMILES string using a simulated
>>>> annealing method. I then pass the resulting structure to an
>>>> OBForceField instance to generate more accurate geometry. However, the
>>>> coordinates in the OBMol operated on remain the same after performing
>>>> the force field simulation. I'm using the UFF force field.
>>>>
>>>> I've used the demo code listed in the OBForceField API documentation,
>>>> and then view the resulting coordinates by
>>>>
>>>> FOR_ATOMS_IN_MOL(atom, mol)
>>>> {
>>>> // ...
>>>> cout << atom->GetX() << ","
>>>> << atom->GetY() << ", "
>>>> << atom->GetZ() << endl;
>>>> }
>>>>
>>>> It is clear from the output that the positions remain identical. Yet
>>>> the OBFF logs a successful convergence:
>>>>
>>>> C O N J U G A T E G R A D I E N T S
>>>>
>>>> STEPS = 1000
>>>>
>>>> STEP n E(n) E(n-1)
>>>> --------------------------------
>>>> 1 141098.938 468447.427
>>>> 6 43405.513 43405.513
>>>> CONJUGATE GRADIENTS HAS CONVERGED
>>>>
>>>>
>>>> Has anyone a suggestion as to why this is happening? Any advice would
>>>> be welcome.
>>>>
>>>> With thanks and kind regards,
>>>>
>>>> David
>>>>
>>>
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