AMBER Archive (2003)

Subject: Re: AMBER: What does this error message mean?

From: Jose Ramon Blas (jramon_at_mmb.pcb.ub.es)
Date: Fri Oct 31 2003 - 18:29:19 CST

This is a typical problem in the setup of the system. The message refers
to atoms 1427 1428 (distance between them is larger than the one expected
from the topology file --> and then SHAKE procedure is the first thing
that crashes). To solve this (2 ideas):

i) look for consistency between your topology-coordinate files (same order
in the atoms)

ii) if consistency is OK, try minimizing your system (to avoid close
contacts between atoms) before starting a fully unrestrained MD.

Hope this helps

Blas

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Jose R. Blas
Molecular Modelling & Bioinformatics e-mail: jramon_at_mmb.pcb.ub.es
IRBB, Parc Cientific de Barcelona phone: + 34 93 403 71 55
C/Josep Samitier 1-5,
08028 Barcelona

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