AMBER Archive (2009)

Subject: Re: [AMBER] partial charge and topology of intrastrand cross-link DNA

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Wed May 27 2009 - 00:27:40 CDT

Dear Shuang,

> I try to perform MD simulations of 11mer DNA duplexes which have
> (1,2) or (1,3) intrastrand cross-links. One of the modified base
> formed bonds directly with nearby base.
> How should I calculate the partial charges of the cross-links and
> define the topology of them?

You can use R.E.D. for that, it generates FF libraries in the Tripos
mol2 file format. You have several options:

- You consider the cross linked bases X-Y as a single residue. This
mean you have to generate the cental fragment, and terminal fragments
as you would do it for a single nucleoside.

- You consider the cross linked bases as two residues X and Y
* You use 2 intra-molecular charge constraints (set to zero) for the
R1 and R2 connecting groups: X-R1 R2-Y
=> You will consequently generate FF libraries for the X and Y
fragments that will be connected in LEaP.
* using a similar approach you use a single inter-molecular charge
constraint (set to zero) for the R1 + R2 connecting groups: X-R1
      R2-Y
=> RED will automatically create a FF library with a connection
between X and Y

This is difficult to answer without having a look at the structure.

regards, Francois

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