Re: [AMBER-Developers] new CVS versions of leaprc.ff99bsc0 and ambpdb.f

From: Joe Krahn <>
Date: Tue, 31 Mar 2009 18:27:00 +0100

David A. Case wrote:
> 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.
My own solution is to have PDB name conversion tables in a data file.
The file can hold any number of naming variations, and makes it easy to
convert among any defined variation. It can also be modified without
recompiling anything.

> (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.
Using CNS, I created my own set of topology files that use PDB version 3
nomenclature. It makes things a lot easier. However, it is not a perfect
solution. PDB v3 has a very badly designed atom name alignment.
Sometime, it follows PDB v2 element-alignment, but other times it does
not. The only way to get it right is to either keep the leading space in
tact everywhere, or to add an additional alignment flag data item. Since
Leap is too inflexible, it will still probably require a data table.

This problem was pointed out to RCSB by many of the people who they
asked to test the v3 nomenclature. However, they intentionally
circumvented the public comment period that had been an established part
of PDB standards before RCSB took over, totally ignoring the needs of
the non-database community. What is even more annoying is that they
don't even want the PDB format (they want to use mmCIF), so there is no
reason not to let us have a significant input.


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Received on Wed Apr 01 2009 - 01:16:18 PDT
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