I put a page on the AMBER wiki describing my current implementation of
storing PDB attributes in the PRMTOP file:
http://ambermd.org/pmwiki/pmwiki.php/Main/PDBAttributes
Feel free to edit it, add comments, etc.
I am writing the X-ray code so that PDB I/O can be used without X-ray
forces, as a conveniences for people that benefit from working with PDB
files containing chainId and resSeq data.
My plan for X-ray is that B-factor and occupancy values are read and
written to PDB files, which exclude all of the bulk-solvent atoms. Those
atoms will not be used in the X-ray forces, so they don't need x-ray
parameters.
This way, no changes are needed for CRD files, Coordinates for X-ray
atoms will be redundant with those in the CRD file. Normally, the CRD
will have priority, and the PDB coordinates are ignored.
Joe
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Received on Wed Mar 25 2009 - 01:16:23 PDT
