AMBER Archive (2002)

Subject: Re: pseudoatoms and NMR restraints

From: David A. Case (case_at_scripps.edu)
Date: Tue Nov 05 2002 - 10:06:07 CST

On Tue, Nov 05, 2002, david wrote:
>
> I have a NMR strucutre of a protein, so I would like to do some
> simulation in AMBER, using my NMR restrains.
> I have not any stereospecific assignment of HB*(QB), HG*(QG),HD*(QD)
> and I have some restraints involve a pseudoatoms
> How could I build my file of restraints in that case ?
>
> for instante,
>
> HA and QB or QG or QD
> HA and methyl group,
> QB or QG or QD and methyl group,
> methyl group and methyl group,
>

This is discussed in section 5.13.2 (pp. 125-128) of the Users' Manual.
Amber NMR restraints are pretty much compatible with those from DYANA or
DISGEO, if you are familiar with those programs.

..dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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