[ghemical-devel] JOELib+Ghemical

[Tommi Hassinen]

On Wed, 25 Jun 2003, Joerg K. Wegner wrote:

> Hello,
>
> I've activated the Java-JNI interface to Ghemical to calculate Tripos5.2
> MM and minimize molecule energy (rotatable bonds). Unfortunately this
> works only under Windows/Cygwin and Linux/IBM-SDK, because SUN's JDK
> causes some internal JNI exceptions (JDK BUG!!!).

Ok, this sounds good; so it seems that making a separate library was a
worthwhile effort!  :)

> Let's see if this will be stable enough to make it available with JOELib.
> At the moment i'll use it only for students in the practical course.
>
> Two more questions:
> 1. Are there real MMFF94 terms definitions available ?

No, there's only the Tripos FF at the moment.

But soon this is going to change, because I'm developing a forcefield of
my own, and as soon as it gets usable I'll make it available as well. I
think it will be a lot better than Tripos but how it compares to MMFF94 we
shall see...

> 2. The partial charge initialization for plain C and c seems to be
> missing, is that correct ?

In fact the charges are dealt in the Tripos implementation like in MMFF94;
that is using "bond-charge increments". So only tabular values are used,
and there is no algorithm to calculate the charges like the Gasteiger one
for example.

Regards,

	Tommi