On Sat, Feb 1, 2014 at 9:33 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> 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.
>
That's what happens in the upcoming version of cpptraj (V14).
>
> p.s.: we should check that the various ways amber writes pdb files all have
> element info on the atom cards.
>
This is also in the next version of cpptraj at least.
>
> p.p.s: still hoping that ambpdb can be replaced with a shell script that
> calls
> cpptraj....
>
This is on my to-do list...hopefully I will get to it soon...
-Dan
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Received on Sat Feb 01 2014 - 09:00:03 PST
