[ghemical-devel] PDB export with ghemical 1.51

[Geoff Hutchison]

On Feb 18, 2005, at 7:01 AM, Tommi Hassinen wrote:

> final. However now I have not changed the format anymore so it seems 
> to be
> OK for now... Following is a sample of the new format (H2O molecule):

A few questions so I can get slightly better code into Open Babel...

> !Info 1 allmm 241
>        ^^^^^^^^^^^	a "setup" class name and an "engine" class ID
> 			for QM. valid "setups" are allmm and allqm.

So for translating from some other format (i.e., PDB) to Ghemical 1.5x, 
this should go default to:

!Info 1 allmm -1

> !Atoms 3
> 0 8 +0 0

Again, so the above line would be a default from another format? Do you 
think it would be useful to assign atom types using the OB atom typing 
code? For example, it'd be possible to translate from Sybyl Mol2 types, 
which would save some time for the user. Of course if you think the 
Ghemical MM types are going to change a lot, this wouldn't be worth the 
effort.

One further request...
I'd *really* like to access the periodic boundaries for file types with 
unit cell information. Is the periodic engine working in the 1.5 tree? 
I don't see a dialogue for setting the boundary parameters.

-Geoff