[Molecularmechanics] Re: Re: Some general remarks.

[Martin Field]

Hi,

Konrad wrote:

> In fact, the main problem of the proposal I made is that it is perhaps too
> flexible. There are many different ways to describe the same system, which
> might make it difficult to compare systems or to apply force field
parameter
> attribution easily.

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.

> But, as discussed recently, there is a solution in the form of explicit
conventions
> for the representation of standard systems (e.g. peptide chains).

> I don't see any difficulty in translating PDB files (at least for standard
> elements) into whatever format we come up with, keeping all the
information
> (in principle) or as much as the authors of conversion programs are
willing
> to deal with (in reality).

> On the other hand, I wouldn't like to see a straight CMLization (line by
line)
> because with little more effort one could produce better structured data.
The
> PDB approach of coding structure as string attributes of atoms is rather
> old-fashioned in my opinion. Moreover, a very straightforward translation,
> changing nothing but syntax, would probably result in the same mess that
we
> have currently, with each program using different atom names and even
> different residue names (e.g. for water).

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.).

> Because the rules for assigning the force field terms are different. For
> example, CHARMM lists improper dihedrals explicitly in the topology
> definitions, whereas AMBER constructs them algorithmically (all possible
> four-atom combinations that have the right bond structure, of which some
then
> might have an prefactor of zero). And then the devil is in the details. It
> was only when I really implemented the AMBER force field that I found out
> that the energy terms depend not only on the bond structure, but also on
the
> alphabetical ordering of atom names.

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.

> The ultimate definition of each of the well-known force fields is still a
> particular program code rather than a formal definition. If anyone wants
to
> analyze these codes to figure out the rules, fine - I am not volunteering
to
> do it!

The fsatom/MM group seems to have participants from many of the major
programs so this shouldn't be a problem.

> The conversion from a hierarchical to a flat representation is nearly
trivial,
> whereas the inverse is a difficult and not even well-defined problem.

Of course.

Cheers,

Martin.