AMBER Archive (2008)

Subject: Re: AMBER: RDCs in AMBER 10

From: Douglas Kojetin (douglas.kojetin_at_gmail.com)
Date: Tue Feb 12 2008 - 19:01:30 CST

Hi Dr. Case,

Thanks for the response. I misread the Amber 9 manual (page 196;
6.12.9; Direct dipolar coupling restraints: makeDIP_RST) and thought
that only N-H and Ca-H RDCs were supported, whereas the limitation is
on makeDIP_RST. I will try to make the modifications to the
makeDIP_RST script to create input files for my other RDC data.

Thanks,
Doug

On Feb 12, 2008, at 6:56 PM, David A. Case wrote:

> On Tue, Feb 12, 2008, Douglas Kojetin wrote:
>>
>> Will AMBER 10 provide support for residual dipolar couplings other
>> than backbone N-H and Ca-H and, although less important, step-by-step
>> weight changes of dwt for RDCs [ http://structbio.vanderbilt.edu/
>> archives/amber-archive/2007/3787.php ] ?
>
> Amber 9 (or 10) are not limited to NH and CaH RDC's: you can use
> whatever
> nuclei pair you want (including H-H RDC's, for example). Take a
> look at the
> files in amber9/test/rdc: this shows RDC's applied to a nucleic
> acid. The
> same ideas could be used for any RDC, as far as I can see.
>
> Amber 10 will also allow for CSA (or pseudo-CSA) constraints to be
> defined;
> these are quite similar to RDC's in their information content.
>
> Using weight changes to ramp dwt up or down has not yet been
> added. But
> thanks for reminding me again about this.
>
> ....regards...dac
>
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