[Molecularmechanics] Re: Re: Some general remarks.

[Konrad Hinsen]

On Saturday 22 November 2003 04:00, Martin Field wrote:

> At least for the specification and comparison of system composition, there
> would seem to be a natural overlap between fsatom/MM and many areas
> of chemi-informatics. In that case wouldn't it be more logical to use or
> build upon some of these technologies? Examples that come to mind include
> smiles, unique smiles and its extensions and IUPAC's IChi.

All I know is smiles, which I think is not sufficient for our needs, and 
difficult to build on. Smiles represents only the elements and the bond 
structure in between them. There is no way to attach any other information, 
not even unique atom names to which one could refer from elsewhere. There 
isn't any support for intra- or supramolecular structure either. From what I 
could find about IChi, it seems to have similar aims as smiles, so I expect 
it to have similar shortcomings for specifying simulation systems.

What I like about XML-based formats is their extensibility, it is always 
possible to add on more information in such a way that programs that don't 
need it can just ignore it. I think this is important in a field that is 
still rapidly evolving.

> Fine. But all conventions can be abused or not adhered too. The problem
> is to make it as easy as possible to use (e.g. automatic generation of
> unknown fragments, of atom names, etc.).

Right. We should not only produce a file format recommendation, but also 
reference implementations and tools for common transformations, to make all 
this as easy as possible.

> The situation with proper dihedrals in some of the old, united-atom CHARMM
> force fields was similar. Such cases will have to be tackled although I
> suspect
> that many force fields have not been validated to such a precision that
> alternative
> "easier" ways of assigning such terms could be substituted.

Certainly, but we have to work out such ways and verify that they are close 
enough in practice.

Konrad.
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