On Sat, Feb 01, 2014, Daniel Roe wrote:
>
> One more thing - note that when you read in the average PDB as a topology,
> since it does not contain mass information, the mass-weighted RMSD will be
> slightly off from what you would expect (all the masses in that topology
> will be set to 1.0).
But we know how to get masses from a PDB file: look at columns 78-79 (I think)
to get the element; or, if those are blank, use rules with the atom name
to generate the element; then populate the masses in the topology from a table
that links element to mass.
Of course, there are some things you can't get from a PDB file, but atomic
masses should generally be available.
...thx...dac
p.s.: we should check that the various ways amber writes pdb files all have
element info on the atom cards.
p.p.s: still hoping that ambpdb can be replaced with a shell script that calls
cpptraj....
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Received on Sat Feb 01 2014 - 09:00:02 PST
