AMBER Archive (2009)

Subject: Re: [AMBER] restraint of REMD

From: Carlos Simmerling (
Date: Fri Jan 16 2009 - 05:57:29 CST

chirality restraints are only needed if you use very high T in the
replicas, it keeps the chirality from inverting. my experience is that
you need these if you are using T over 400-500 or so. lower T doesn't
need it, so it will depend on the T range you have decided to use.

I don't know if there is a program to create such restraints for RNA,
maybe someone else on the list does.

On Thu, Jan 15, 2009 at 9:51 PM, z g <> wrote:
> Dear sir :
> I have seen the tutorials of Replica Exchange Simulations with
> AMBER 10 online. I have some questions about Generating chirality restraints
> Whether I must restraint the moleculars before I do the REMD on high
> temperatures?
> I want to do the REMD on RNA, Whether the program "makeCHIR_RST"
> suitable for RNA? How can I do this ?
> Thank you !
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