[AMBER] Dihedral restraint problems in AMBER16/18

From: Rebecca Twidale <rebecca.twidale.bristol.ac.uk>
Date: Fri, 14 Feb 2020 12:33:56 +0000

Dear AMBER users,

I was just wondering if anyone has experience with running umbrella sampling on a dihedral angle in either AMBER16 or AMBER18? I’m currently trying to do just that and I’m having problems with what is being written to the trace file. I’m stepping from 60 degrees to 180 degrees, and my r1 and r4 values are minus and plus 180 degrees respectively in each rc window. For the majority of RC windows, it just outputs 0 to the trace file, but otherwise, it outputs the value I would expect to the trace file. There does not seem to be any pattern to when it correctly writes the restraint values to the trace file.

My restraint file is as below:



 r1=-120.0, r2=60.0, r3=60.0, r4=240.0,

 rk2=100, rk3=100,


I have attempted to run the same simulation in AMBER14, 16 and 18. The problem only occurs in AMBER16 and AMBER18. Unfortunately I cannot get around the issue by using AMBER14 because I am using DFTB3, which is not available in AMBER14.

Do you know if this is a known problem for the later versions of Amber and if there is a way to fix this problem?

Best wishes,


Rebecca Twidale

TMCS PhD Student
Mulholland Research Group
Centre for Computational Chemistry
School of Chemistry - University of Bristol
Bristol BS8 1TS - United Kingdom

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Received on Fri Feb 14 2020 - 05:00:02 PST
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