[AMBER] Bug Encountered When sourcing GAFF in leap.in

From: Vollmers, Luis <luis.vollmers.tum.de>
Date: Tue, 16 Nov 2021 15:28:27 +0000

Hi everyone,

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 positions.

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.

I can supply the files that produced the 'bug' if necessary.

Why does sourcing gaff result in the wrong NTYPES?

How is it possible that the resulting parameters produce a system that seems to be frozen?

Can you source gaff without this issue?

All the best,

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Received on Tue Nov 16 2021 - 07:30:03 PST
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