[AMBER-Developers] PDB attributes for PRMTOP files

From: Joe Krahn <krahn.niehs.nih.gov>
Date: Tue, 24 Mar 2009 16:53:04 +0000

I put a page on the AMBER wiki describing my current implementation of
storing PDB attributes in the PRMTOP file:

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

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.


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Received on Wed Mar 25 2009 - 01:16:23 PDT
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