Re: [AMBER] regarding forcefield for rna

From: Asfa Ali <>
Date: Mon, 14 Jun 2010 10:27:40 +0530


I have used a 20 ps heating(MD1), six equilibration steps of 50 ps except
MDe6 which is of 1 ns where I have reduced the restraints from 50 kcal/mol
to 5 followed by a final prodn run of 6 ns without restraints.

The pdb file 2kbp is an intermolecular RNA G-quadruplex. I guess since it is
an intermolecular G-quadruplex therefore this sort of opening up is taking

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Received on Sun Jun 13 2010 - 22:00:04 PDT
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