Peptide not flexible in docking

HADDOCK
1

Hi,
I built a peptide using pyPept but unfortunately, when I dock the peptides with my protein HADDOCK is unable to change the conformation of the peptide (the peptide in the docking results are too similar to the starting structure).
I changed the following parameters in the run.cns file, are there any other parameters I should change?
And just to ensure, did I define the fully flexible peptide correctly? it is segid B and set to malecule 2 (or should I have changed nfle_2 also?
I am using restraints of active and passive residues and local version.

Thank you!

{* Fully flexible segments for molecule 2 }
{ Note that current max is 5 (edit the run.cns to add more segments }
{===>} nfle_2=0;
{ Residues of molecule 2 at interface *}
{+ table: rows=5 “segment 1” “segment 2” “segment 3” “segment 4” “segment 5” cols=2 “Start residue” “End residue” +}
{===>} start_fle_2_1=“5”;
{===>} end_fle_2_1=“16”;

{* number of MD steps for rigid body high temperature TAD }
{===>} initiosteps=2000;
{ number of MD steps during first rigid body cooling stage }
{===>} cool1_steps=2000;
{ number of MD steps during second cooling stage with flexible side-chains at interface }
{===>} cool2_steps=4000;
{ number of MD steps during third cooling stage with fully flexible interface *}
{===>} cool3_steps=4000;

2

Your should set nfle_2=1 is this case if you want your peptide to be fully flexible.

3

Thank you!
Does that mean then that it didn’t change the peptide to flexible from amino acids 5-16? since I didn’t do
{===>} nfle_2=1;

4

Yes indeed

5

OK
But the docking results came out differently when I used flexible (in the wrong way) or didn’t use them. Is that because Haddock has some randomness involved? or it does still make some difference.

6

There is indeed some chaotic nature to this type of computations, especially if run on different hardware. But I would not expect major differences unless some other parameter settings are changed.

And if you kept default settings for the semi-flexible segments your peptide would have some flexibility anyway