[Molecularmechanics] Recycling CML

[David van der Spoel]

On Wed, 5 Nov 2003, Peter Murray-Rust wrote:

>>What are the modifications that are possible with that mechanism? I am
>>thinking of the modifications that David presented in his proposal, for
>>defining variants of fragments (e.g. the N-terminal variant of an amino acid
>>residue). Such a modification involves adding and removing atoms and bonds.
>
>There are 3 main modes:
>- override/overwrite (replace existing values with new ones, but keep those 
>without replacement values)
>- merge - add in new information where is does not conflict with previous
>- replace - replace existing molecule with the new information without 
>retaining any of the old info
>
>Therefore bonds could be deleted by using the last mode.
>
>The design was intended to provide different snapshots (for whatever 
>reason) of a molecule. The initial impetus was dynamics and conformations - 
>things like element type and bonds would be kept constant. But there is no 
>reason why bonds should not be changed.
>
>The design was originally to create different instances of the same 
>molecule, but there is no reason in principle why it shouldn't be used to 
>clone them as well.
>
Sorry, which "the design" are you referring to? (I may have missed it in
an earlier mail though...)

The three options you describe are basically in my proposal. I don't see
why my proposal should be limited to linear and/or peptide chains (as
Konrad suggested), it is flexible in the sense that it defines a framework
for describing different types of linkages (should work for any polymer
and any type of crosslinking) and also for modification of any group.

A good specification in XML format could also serve as a template for
implementing the algorithm (and we already have an algorithm like it in
GROMACS, so it is possible)

>BTW - I may seem overcautious  - feel free to ignore this:-). So long as 
Maybe I am over optimistic (it wouldn't be the first time...)

David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel@xray.bmc.uu.se	spoel@gromacs.org   http://xray.bmc.uu.se/~spoel
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