Force field and scoring function

HADDOCK
1

Hi,
I read a lot of HADDOCK background and I want to ensure I understood correctly- the forcefield used in haddock2.4 local version is OPLSX non-bonded parameters, while there is an option to use the course-grained I specified. Correct?
{* Coarse grained molecule? *}

Also, I have seen this figure on violations for AIR, but how are the violations calculated from unambiguous restraints?
And I will very much appreciate the source article.

image
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Thank you very much

The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab

2

Hi Michael,

Yes indeed

Yes, in that case, first the structure is being coarse grained with Martini2.2 and the corresponding force-field is used.

Here is the reference:
D.H. de Jong, G. Singh, W.F.D. Bennett, C. Arnarez, T.A. Wassenaar, L.V. Schäfer, X. Periole, D.P. Tieleman, S.J. Marrink
Improved Parameters For The Martini Coarse-Grained Protein Force Field, J. Chem. Th. Comp, 9:687–697, 2013. DOI:10.1021/ct300646g

With the hope these answers will help you.

Cheers

3

Thank you
So how are there restraints violations (positive NOE violations + Eair) if I only use unambiguous restraints?
how are those calculated?
My understanding is that constraints always have to be obeyed, and they are not always

4

Actually unambiguous restraints can be violated in the same way as ambiguous restraints. And violations will depend on the effective distance being calculated compared to your restraint range definition

michael:

how are the violations calculated from unambiguous restraints

There are none. Unambiguous restraints should be considered more as constraints.

With the hope these answers will help you.

Cheers

5

I’m sorry, but I don’t understand
From what I know constraints mean they cannot be violated, therefore how can you say
“Actually unambiguous restraints can be violated in the same way as ambiguous restraints. And violations will depend on the effective distance being calculated compared to your restraint range definition”
From this sentence, it seems there can be a violation (and therefore I see in the results that there are violations even though the only restraints I use are unambiguous)

6

Because they are restraints and not constraints

7

but you wrote also
" Unambiguous restraints should be considered more as constraints ."

I’m sorry for this confusion, I don’t understand

8

This was a mistake - they are restraints!
Sorry for the confusion

9

I am very sorry michael that you got confused, I guided you wrong.
I just learned something here.
I modified my first post so future user will no more get confused.

10

thank you
Ok so this is the function

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If I have a restraint were the distance allowed is “3.3 1.0 1.0” (so the range is between 2.3 and 4.3), how will the value of this function be implemented in the docking scoring Eair? I can’t find anywhere the full calculations. Is this on purpose?
If not can you please explain/ send a source article?
Thank you

11

See: https://ask.bioexcel.eu/t/how-is-eair-calculated/4085

And remember the forum is searchable :slight_smile:

12

Hi,
I just want to make sure- the “X” in OPLSX stands for some extension/ version that I’m assuming HADDOCK forum will not share?

13

No - it is the standard version which has been used e.g. for NMR structure calculations and distributed with HADDOCK as described e.g. in:

14

Thank you
So what does the X stand for? explicit? Since I do not see the word OPLSX in the article.

15

Historical naming… I actually don’t know if X has a special meaning.