AMBER Archive (2004)

Subject: AMBER: Diastereoisomers of ATP

From: William Boxford (web100_at_york.ac.uk)
Date: Thu Nov 18 2004 - 09:18:42 CST

Hello,

we are currently running some gas-phase simulations of ATP and related
molecules with Sander. We appear to be having some problems whereby within
one time step of a given simulation the Ribose ring changes to another
diastereoisomer. This seems rather strange as it strikes us to be a
physically impossible change.

We would like to know if anyone has encountered a similar situation, and if
anyone knows how to ensure that this change cannot occur. We have already
tried running Sander with a variety of temperatures, time steps and other
parameters.

Many thanks,

William Boxford,
University of York.

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