[Molecularmechanics] Recycling CML

[Konrad Hinsen]

On Friday 07 November 2003 17:25, Pengyu Ren wrote:

> I just took a quick look at the two proposals by you and David. David's
> certainly more specific to protein. In your proposal two however each
> residue/fragment is a "molecule" (why can't we just call it fragment?).
> It's then easy to make a new molecule by resuing fragment libraries.

They are indeed fragments, and the "templates" part of the file is a fragment 
library that could also reside in a separate file. The term "molecule" is 
used because that's what CML uses.

> I noticed your concern about definition of fragment, which may be force
> field dependent. For protein, my suggestion is to use the whole residue as
> a fragment, which makes interchanging force field a _lot_ easier. For any

The whole residue is a fragment in my file, the fact that it is itself divided 
into two fragments is not really a problem since expansion is easy - the 
tricky part is to know which fragments are residues and which aren't. BTW, 
the subdivision is quite useful in practice, e.g. for identifying the 
backbone. If you don't put the division into the definition file, it will end 
up as explicitly coded chemical knowledge inside many programs, which is a 
less flexible approach.

> other new molecules and new force field, whoever develop it should give the
> definition of fragments and corresponding parameter files in such format.

That sounds like a reasonable compromise: standardize names and layouts for 
frequently used items, and leave the rest open, possibly to be standardized 
in the future if and when a need arises.

> For protein modeler, I propose we also define a format for paramter file.
> We only need one copy of it. It should contain all the amber, charmm, ,,,
> paramters, fuctions in the format corresponding to the structure file

We have discusses this a bit already. I would prefer to postpone this for now, 
because of the compatibility issues in the force field definitions. For 
example, a "partial charge" does not mean exactly the same in Charmm and 
Amber, because Amber a 1-4 factor on electrostatic interactions which affects 
the total electrostatic energy. I expect the definition of a universal set of 
parameters to be a lengthy task.

Konrad.
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