At 14:18 20/12/2006, [EMAIL PROTECTED] wrote:
On 19 Dec, peter murray-rust wrote:
> If what you meant is "can we have an open database of 3D structures,
> the answer is a qualified 'yes'" - without taking them from CSD.
> There are two main methods:
> * extract them from non-copyright crystal structures (there are a lot
> of these and we are collating them - watch this space.
> * create them from connection tables. There are various levels of
> "accuracy" including forcefields and theochem methods. We have done
> this for 200,000 molecules - see
> http://www.dspace.cam.ac.uk/handle/1810/724 If you are happy with
> PM3, then use these
What is pm3?
The Hamiltonian in MOPAC (essentially the level of accuracy and cost
of computation - e.g. AM1 is cheaper and less accurate).
I noticed that the coordinate files are stored in cml
format, which we can presumably translate to pdb for our needs with Open
Babyl.
OpenBabel. Yes.
P.
Peter Murray-Rust
Unilever Centre for Molecular Sciences Informatics
University of Cambridge,
Lensfield Road, Cambridge CB2 1EW, UK
+44-1223-763069
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