DNA ending effect

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Hello everyone

I have a question regarding DNA simulation

How to restrain the terminal ends to avoid the ending (Fraying ) effect due to the lack of WC structure at the ends of the DNA duplex?
How can I modify the top file to do so?

Thank you so much

Use distance restraints to enforce the hydrogen bonds between terminal base pairs.

Thank you, Justin!
Do I need to merge the two DNA topologies, then define groups in an index file that represent the heavy atoms in the terminal base pairs?

You need a merged topology but no special index groups. Distance restraints are defined within the topology (using the merged [moleculetype] definition) and thus no index group is needed.

Thank you again, Justin.

so then I need to add the following code to the [bonds] section of the topology file to keep the terminal base pairs (T-A) hydrogen-bonded

; atom_i atom_j func r0 r1 r2 k(kJ mol^-1 nm^-2)
20 3602 10 0.0 0.5 0.6 10000
21 3605 10 0.0 0.5 0.6 10000

20,21 , 3602, 3605 are the residue numbers of the heavy atoms

Am I doing this correctly?

Thank you again for your help

Those lines do not belong in a [bonds] directive, they belong in [distance_restraints].

So, I need to create a new section [distance_restraints] , and copy these lines, right?

Thank you so much, Justin, for your generous help.

Yes, see the manual.

I was reading the manual, I found this:

For restraints not derived from NMR data, this functionality will usually suffice and a section of [
bonds ] type 10 can be used to apply individual restraints between pairs of atoms, see Topology file
(page 406). For applying restraints derived from NMR measurements, more complex functionality
might be required, which is provided through the [ distance_restraints ] section and is
described below.

The distance restraints I used were not derived from NMR experiments. So If I understood correctly, I need to add those lines to the bond section? I am confused

The mathematical form of distance restraints is taken from NMR structure fitting, so it can directly interface with experimental data, but there is no requirement to do so. You can achieve the same thing a number of ways, e.g. type 10 bonds, pull code, etc. However you do it is up to you.

Got it!

Thank you so much, Justin

Another approach is using the “pull” distance constraints between terminal bases. In this case, we can use standard topologies.
We discussed this problem earlier: Constraining terminal basepairs in DNA


I had this same issue. I went into it in the post that genie alluded to. Genie gave a great example of how to do the “pull” function and I tried my best to go into detail with how to do the approach that Justin suggests. In case you missed the link above:

Thank you so much. will try that!