creating tbl file

[pallavi-compchem]

Hi there,

I am unable to find an explanation of the tbl file for imposing interaction restraints. Could you please help understand the format of the tbl file and how to create such files?

Thanks.

Best, Pallavi

[VGPReys]

Hi Pallavi,

Please refer to the Nature Protocols and Nature Protocols Correspondence paper where everything is well described. Also, you can use our GenTBL online tool to generate a restraints file based on residues ids.

Cheers

[pallavi-compchem]

Hi,

Thanks for the links! I have now an understanding of the general syntax, but I still have one question. In the protein-DNA docking example, the cro_air.tbl shows:

assign ( resid 27 and segid A) ( ( resid 32 and segid B and (name O2 or name O4 or name H3 or name C2 or name C4 or name C5 or name C6 or name C7)) or ( resid 33 and segid B and (name O2 or name O4 or name H3 or name C2 or name C4 or name C5 or name C6 or name C7)) or ( resid 34 and segid B and (name N3 or name N7 or name O6 or name H1 or name H22 or name H21 or name C2 or name C4 or name C5 or name C6 or name C8)) ) 2.0 2.0 0.0

Does this imply that center of mass of the residues connected by "or" (residues 32, 33, 34) is used for the distance restraint?

[amjjbonvin]

No - it does not. The effective distance is calculated as:

[Sum (1/r6) ](-1/6)

over all pairwise distances between all atoms in the selections.

On 24 Apr 2024, at 16:30, Pallavi Banerjee @.***> wrote:

Hi,

Thanks for the links! I have now an understanding of the general syntax, but I still have one question. In the protein-DNA docking example, the cro_air.tbl shows:

assign ( resid 27 and segid A) ( ( resid 32 and segid B and (name O2 or name O4 or name H3 or name C2 or name C4 or name C5 or name C6 or name C7)) or ( resid 33 and segid B and (name O2 or name O4 or name H3 or name C2 or name C4 or name C5 or name C6 or name C7)) or ( resid 34 and segid B and (name N3 or name N7 or name O6 or name H1 or name H22 or name H21 or name C2 or name C4 or name C5 or name C6 or name C8)) ) 2.0 2.0 0.0

Does this imply that center of mass of the residues connected by "or" (residues 32, 33, 34) is used for the distance restraint?

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[pallavi-compchem]

Ok, understood!

Also, what is the difference between Haddock restraints for 1st partner vs those for 2nd partner? Can't we put all the restraints in one section? For the same protein-DNA docking example, I see the following under "HADDOCK AIR restraints for 1st partner": assign ( resid 27 and segid A) ( ( resid 32 and segid B and (name O2 or name O4 or name H3 or name C2 or name C4 or name C5 or name C6 or name C7)) or ( resid 33 and segid B and (name O2 or name O4 or name H3 or name C2 or name C4 or name C5 or name C6 or name C7)) or ( resid 34 and segid B and (name N3 or name N7 or name O6 or name H1 or name H22 or name H21 or name C2 or name C4 or name C5 or name C6 or name C8)) ) 2.0 2.0 0.0 !

and the following under "HADDOCK AIR restraints for 2nd partner": assign ( resid 34 and segid B and (name N3 or name N7 or name O6 or name H1 or name H22 or name H21 or name C2 or name C4 or name C5 or name C6 or name C8)) ( ( resid 27 and segid A) or ( resid 29 and segid A) ) 2.0 2.0 0.0 !

Residues 27, 29, 34 are mentioned twice.

[VGPReys]

The first selection is called active residue, while the second selection is called passive residue.

Restraints penalties only apply on active residues.

Therefore having the reverse (in the "HADDOCK AIR restraints for 2nd partner"), allows to define previously described passive (from chain B) residues as active, and vice-versa.

[pallavi-compchem]

Got it! Thanks :)