Fully flexible segments in local setup

HADDOCK
1

Hi,

I am trying to dock a single protein to a complex (using several molecules / pdbs as input). I want several segments as fully flexible.
On the webserver this setup works and the segments are moving as expected. However, using the same configurations in run.cns locally, the parts are not moving at all. It seems to work if I do one of the segments separately, but not all of them together.
I don’t know where this is going wrong. I can share with you a link to my run on the webserver if that helps.

Thanks,
Swantje

2

Compare the run.cns from the server run with your local one

The server is running the same version of HADDOCK as distributed for local usage (latest is 2.4 January release)

3

I ran it locally in the folder from the server and things did not move.
However, our HADDOCK 2.4 is from September, so maybe something changed? I am currently waiting for the download and then run it again with the newest version.

4

I ran it locally in the folder from the server and things did not move.

Did you compare the run.cns settings???

However, our HADDOCK 2.4 is from September, so maybe something changed?

No changes that can explain your problem.

You must simply be missing some settings in the flexibility.

5

PS: The server uses by default the automatic flexibilty setting (unless changed by the user).

And the online manual page for flexibility-related settings is:

https://www.bonvinlab.org/software/haddock2.4/run/#definition-of-the-semi-flexible-interface

6

Apologies for the misunderstanding. I checked and changed differences in run.cns. Moreover, I cleaned the folders of the webserver run and ran locally using the webserver’s run.cns, and in the local version, the flexible segments did not move.

7

Can you then share your server and your local run in some way (via some link sent via email)?

And just to be sure, you are using the 2.4 version?

8

PS: In which directory are you looking to see if there are changes in structure?

9

I sent a mail with a local run and the link to the server run. I am checking structures/it1 for the changes. Thanks already for looking at this!

10

For your test run (run4) most structures (9/10) at it1 failed and accordingly only a minimisation was performed (you can see that from the presence of .fail files in that dir).
The only one that has not failed is model 9 - check if the loops have moved.

In the server run 146 of 200 it1 models also failed and only underwent a minimisation. The other ones went through and probably score better

11

There can be many causes for those failures, e.g.:

  • bad geometries of the starting models (e.g. clashes)
  • “strong” / bad restraints

Sometime decreasing the temperature of the simulated annealing at it1 might help.

12

Yes, you are right, model 9 did work - I must have missed it when opening all together.
Thank you so much!