[Molecularmechanics] Request for comments

[Konrad Hinsen]

On Friday 07 November 2003 19:54, Peter Murray-Rust wrote:

> >What do you mean by "crystallographic topology" files, and how are they
> >related to forcefields?
>
> They are used in constrained refinement and simulated annealing/MD methods
> for Xray refinements (tools like X-PLOR are direct descendants of (I think
> CHARMM)).

I see. Yes, those are very similar tools to our simulation codes. X-PLOR uses 
the CHARMM force field, perhaps even the same input file.

> Crystallographers have to create these topological dictionaries for each
> new fragment - cf the HET dictionary of the PDB. They have to define the FF
> parameters (or pseudoFF parameters) for each HET group. The relevance is
> that if you have an unusual fragment in the molecule then it may well have
> been described in this way. It probably reflects that my experience has
> been slightly more in this field that unconstrained MD.

The situation is exactly the same. But I don't think we should make too much 
of an effort to stay compatible with such designs, which are quite old and 
not very flexible by today's standards. The main effort in producing those 
files is in obtaining the parameters, not in putting them into some format. 
Conversion, even manual, would not be much of an effort. I'd rather make a 
format future-proof than backward-compatible.

Konrad.
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