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
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
Received on Tue Nov 05 2002 - 08:06:07 PST
