[gmx-developers] Re: CML and macromolecules
lindahl at csb.stanford.edu
Mon Oct 20 04:48:58 CEST 2003
I strongly second David's comments; in Gromacs we want to use the files
for two purposes:
1. Topology description of the system. CML works great for this, and I
plan to completely get rid of our own topology file format, but then we
probably need a parser that compares e.g. PDB files with a library of
structures and constructs bonds that we know are correct instead of
only using coordinate proximity. This is probably no big deal since we
will anyway have to do it for changing termini, etc...
2. For structure prediction other non-simulation approaches we often
need to do computations on hundreds of structures, but we want to
retain every single piece of information in the PDB files we started
from. Personally I would like to keep comments too, and even stupid
numbering errors, so we can throw away the PDB files.
>> However I think there is still a strong "PDB-like" approach and I am
>> to extend CML to manage that aspect of macromolecules. I think it's
>> useful for CML to try to model protein hierarchy
>> (primary/secondary/supersecondary/tertiary/quaternary, etc.) However
>> could be useful to have a "flat-file" approach" where the atoms had
>> like info on:
>> - their PDB type (CA, SG. etc.)
>> - their PDB number
>> - their residue type
>> - the chain number.
>> CML could carry this - and more - , but would not support the explicit
That would be great - I agree CML works best as a format for low-level
chemical information and not include structural properties. As long as
it is there in one way or another we can write it back to files if we
really need to.
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