Different violation results in ana_noe_viol_all.list and ana_noe_viol_ambig.lis

HADDOCK
1

Dear all,

I defined 6 active residues for Haddock2.2, so I have 6 ambiguous restraints and NO unambiguous restraint or Hbond restraint.

After docking, in the it1/water/analysis fold, there are two files:

ana_noe_viol_all.lis is for the violations of ambiguous restraints and unambiguous restraints.

ana_noe_viol_ambig.lis is for the violations of ambiguous restraints.

Because I only defined 6 ambiguous restraints, these two files should be the same. But the files gave me different Rave and violations, and only part of the ambiguous restraints is present in ana_noe_viol_ambig.lis, while all of 6 ambiguous restraints is present in ana_noe_viol_all.lis.

For ana_noe_viol_all.lis,
Rexp= 2.000 Rave= 2.916 Viol= -0.916 #viol= 275 ( A 102
Rexp= 2.000 Rave= 2.352 Viol= -0.352 #viol= 335 ( A 12
Rexp= 2.000 Rave= 2.309 Viol= -0.309 #viol= 244 ( B 272
Rexp= 2.000 Rave= 2.284 Viol= -0.284 #viol= 159 ( A 103
Rexp= 2.000 Rave= 2.096 Viol= -0.096 #viol= 128 ( B 106
Rexp= 2.000 Rave= 2.094 Viol= -0.094 #viol= 15 ( B 273

For ana_noe_viol_ambig.lis
Rexp= 2.000 Rave= 3.099 Viol= -1.099 #viol= 75 ( A 102
Rexp= 2.000 Rave= 3.002 Viol= -1.002 #viol= 26 ( A 12
Rexp= 2.000 Rave= 2.715 Viol= -0.715 #viol= 18 ( B 272
Rexp= 2.000 Rave= 2.343 Viol= -0.343 #viol= 47 ( A 103

Why?

Thanks a lot for your help!

2

For the first analysis with all restraints the cutoff for printing violations is set to 0.025 to have a long list while it is 0.3A for the individuals sets…

I would not worry about a violation of 0.1A :slight_smile:

3

Thanks for your reply!

There are fewer (only 4) restraints in ana_noe_viol_ambig.lis, because the #violations of the other 2 restraints is 0, which will not be list in the file?

4

for the ana_noe_viol_ambig.lis, only violation > 0.3A are listed, which is why the others are not showing.