[AMBER] 10. QM/MM/MD g09 interface issues, now tleap

From: David Poole <thepoole.ucdavis.edu>
Date: Sun, 11 Dec 2016 19:42:03 +0100

So, it appears that tLeap has a few issues reading in the correct name
for the metal centers, reading only the first letter of the atomic
symbol. In this case, Z is nonsense so it left the field as empty and
so the interface wrote nulls to the g09 input which caused it to die.

I've had this problem as well with palladium, which reads as
phosphorus, as well as iron, reading is fluorine.

This is probably only an issue for QM inclusive calculations, but it
means adjusting the element via the set command as a work around. I
might look into the code later but first I need to modify the
interface more to add a few features for my work.


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Received on Sun Dec 11 2016 - 11:00:03 PST
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