Re: [AMBER] Bug Encountered When sourcing GAFF in

From: David A Case <>
Date: Tue, 16 Nov 2021 11:56:14 -0500

On Tue, Nov 16, 2021, Vollmers, Luis wrote:
>I encountered strange behaviour of my system whose source of error
>seems to be the 'source leaprc.gaff' command line. The system is a
>DNA-Polymerase-DNA-Complex with OPC water and some Ions (T=314K). Sourcing
>gaff resulted in a very rigid trajectory that looked almost frozen. Even
>the water molecules do not diffuse but merely vibrate around their initial
>Not sourcing gaff fixes the problem and the diffusive behaviour returns to
>'normal'. Upon comparing the MDOUT files it became apparent that the VDW
>and electrostatics were unphysical for the gaff-sourced system and upon
>comparing the PRMTOP created by tleap it became apparent that the NTYPES
>are different and therefore different parameters were assigned.

Can you at least post your leap inpput script? It's possible that the order
in which leaprc.gaff is loaded might lead to some weird behavior with OPC.
Reading between the lines, it looks like your system doesn't need GAFF
parameters -- is that correct?

That said, what is reported is odd: leaprc.gaff only loads parameters that
have lower-case atom types, so it should not interfere with other things.
But "bugs" often don't obey the rules they are supposed to follow :-)


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Received on Tue Nov 16 2021 - 09:00:03 PST
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