Re: [AMBER] To fix dihedral angles during a simulation.

From: case <>
Date: Sat, 26 Feb 2011 16:47:44 -0500

On Fri, Feb 25, 2011, Baptiste Legrand wrote:
> After running antechamber, I create random structures of an organic
> compound with an initial heating stage at 1000K for example (to solve
> NMR structures). Nevertheless during this stage and a short minimization
> few peptide bonds became cis instead of the usual trans configuration.
> What is the best way to fix this? to add dihedral restraints?

yes...adding dihedral restraints is appropriate here. The script makeCHIR_RST
will do this for you (see Section 6.7.3 of the Users' Manual). It also adds
constraints to prevent chirality flips during high-temperature annealing,
which is usually what you want. Check the output file before using,
especially if you have any peptide bonds that *should* be cis.

...good luck....dac

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Received on Sat Feb 26 2011 - 14:00:04 PST
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