Specifying sidechain NOE restraints in Relax!

[Anonymous]

Hi,
I have both backbone NOE and sidechain NOE data for a small protein. When I specify the backbone NOE data during Abinito simulation it works fine with scoring penalties displayed in atom_pair_constraints column. But when I modify the constraints file for sidechains and supply it Relax or Score with “-constraints” flag it doesn’t seem to make any change in the energies, I seriously doubt that It takes those constraints into account during relax. So my questions are:
1. Can relax take sidechain restraints?
2. Is there any special flag to supply during relax?
3. Is there a different format for supplying NOE restraints during relax?

Thanks,
Kala

######Abinitio NOE restraints######### (***works)

AtomPair CB 80 CB 69 BOUNDED 0.0 7.0 0.001 0.5 NOE; dist 7.0 0.0
AtomPair CB 80 CB 76 BOUNDED 0.0 7.0 0.001 0.5 NOE; dist 7.0 0.0
AtomPair CB 80 CB 76 BOUNDED 0.0 7.0 0.001 0.5 NOE; dist 7.0 0.0
AtomPair CB 80 CB 69 BOUNDED 0.0 7.0 0.001 0.5 NOE; dist 7.0 0.0

#########################################

#######Side Chain NOE restraints########## (***Doesnt work***)
AtomPair 1HD1 80 1HB 69 BOUNDED 0.0 5.0 0.1 0.5 NOE; dist 5.0 0.0
AtomPair 1HD1 80 2HB 69 BOUNDED 0.0 5.0 0.1 0.5 NOE; dist 5.0 0.0
AtomPair 1HD1 80 3HB 69 BOUNDED 0.0 5.0 0.1 0.5 NOE; dist 5.0 0.0
AtomPair 2HD1 80 1HB 69 BOUNDED 0.0 5.0 0.1 0.5 NOE; dist 5.0 0.0
AtomPair 2HD1 80 2HB 69 BOUNDED 0.0 5.0 0.1 0.5 NOE; dist 5.0 0.0
AtomPair 2HD1 80 3HB 69 BOUNDED 0.0 5.0 0.1 0.5 NOE; dist 5.0 0.0
AtomPair 3HD1 80 1HB 69 BOUNDED 0.0 5.0 0.1 0.5 NOE; dist 5.0 0.0
AtomPair 3HD1 80 2HB 69 BOUNDED 0.0 5.0 0.1 0.5 NOE; dist 5.0 0.0
AtomPair 3HD1 80 3HB 69 BOUNDED 0.0 5.0 0.1 0.5 NOE; dist 5.0 0.0
AtomPair 1HG2 80 1HB 69 BOUNDED 0.0 5.0 0.1 0.5 NOE; dist 5.0 0.0
#############

[Anonymous]

What flaq are you using?

-constraints is an option grouping, and shouldn’t work for any protocol.

-constraints:cst_file is for *centroid* mode constraints, so would work with (certain stages of) abinitio, but wouldn’t work with full atom protocols like relax or (full atom mode) scoring.

-constraints:cst_fa_file is the option you’d want to use for full atom protocols like relax.

[Anonymous]

Thank you very much for the magic flag option.

[Author]

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