On Mon, Aug 05, 2013, Hailin Huang wrote:
>
> I used tleap to generate the top files. The following is the script. I
> think the DX, DY, DZ atoms are complexed with the Mg ions (like the EPW in
> water molecules?), but I have no idea what they are and why the mass is 3...
Use the "desc" command in LEaP to find the elements and masses of your DY1
(etc.) atoms. I'm not sure what is in md6.off (I don't need to know, but you
should check this). As a wild guess, this is some sort of Magnesium atom
with "extra points" (whose mass is 3.0).
> > > Warning: Could not determine atomic number from mass (3.000000) [DY1 ]
> > > Warning: Could not determine atomic number from name [DY1 ]
I think this is just a warning: as you found, the output PDB file will be
garbled because cpptraj doesn't know what element this is. I'm not even sure
what the correct PDB convention should be for a "dummy" atom (if that is
indeed what one has here). It's not clear (to me!) why/how or if this should
break the autoimage command.
...dac
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Received on Tue Aug 06 2013 - 05:00:02 PDT
