I've updated the CVS versions of leaprc.ff99bsc0 and ambpdb.f, to more
correctly represent PDB format version 3.
You should be able to load a version 3 pdb file with either RNA or DNA
(or both!) and have it correctly read.
You should also be able to run "ambpdb -bres" to get output pdb files
that look like PDB version 3 files.
Please let me know about problems, or just fix them! But be aware that
these changes may break some scripts that expect the older formats.
Two further notes:
(1) the new leaprc file may not work as well with older (PDB version2)
input files; more work needs to be done to figure out how to handle the
general problem of potentially having multiple formats for input.
(2) right now, I am using the PdbResMap and PdbAtomMap facilities to map
PDB names to internal Amber names. But it would be much simpler to
modify the Amber libraries (e.g. all_nucleic94.lib) to use the PDB names
natively (we're close, but not exact). That would involve a bigger
change than just modifying a leaprc file, so comments on how best to
handle such a change are welcome.
...thx...dac
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Received on Wed Apr 01 2009 - 01:15:40 PDT
