[gmx-users] about the repelling of DNA base pair

[He, Yang]

Hi, I just got this CG DNA model from a paper as well as the required parameters . What you think I should deal with the interactions about hydrogen bonding ? I have defined all the atoms' charge as 0 but still the repelling happened.

Yang
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
Sent: Thursday, February 05, 2009 3:58 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] about the repelling of DNA base pair

He, Yang wrote:
> Hi all users,
>
> I am dealing with  the CG DNA model and I just list the parameters for non-bond potential blow:
>
>   A     T         1        0.0069        0.000004109
>
>   P     P         1        0.000004352   4.352E-12
>
>   S     S         1        0.000004352   4.352E-12
>
>   A     A         1        0.000002177   1.0894852E-12
>
>   T     T         1        0.000002177   1.0894852E-12
>   C     G         1        0.0097        0.000005422
>   C     C         1        0.000002177   1.0894852E-12
>   G     G         1        0.000002177   1.0894852E-12
>
>   A     S         1        0.000004352   4.352E-12
>
>   A     P         1        0.000004352   4.352E-12
>   A     C         1        0.000002177   1.0894852E-12
>   A     G         1        0.000002177   1.0894852E-12
>
>   T     S         1        0.000004352   4.352E-12
>
>   T     P         1        0.000004352   4.352E-12
>   T     C         1        0.000002177   1.0894852E-12
>   T     G         1        0.000002177   1.0894852E-12
>   C     S         1        0.000004352   4.352E-12
>   C     P         1        0.000004352   4.352E-12
>   G     S         1        0.000004352   4.352E-12
>   G     P         1        0.000004352   4.352E-12
>
>   S     P         1        0.000004352   4.352E-12
>
> You can see that the base pair potential is larger than the other pairs . But I found when I run this case,using the command "ngmx",  it always shows that the matching base pair will repel from each other even I set the temperature by 0K in the mdp.file . I have checked the base pairs' distance and originally they are all in the equilibrium distance.
>

Then your model physics are unrealistic.  Either the parameters are wrong, or
your .mdp options are inappropriate.  Do your nucleotides really just consist of
three particles (base, sugar, and phosphate)?  If so, you may be missing some of
the subtleties of hydrogen bonding (which is an electrostatic interaction), and
the geometry within the helix, and perhaps even causing excessive repulsion
between the phosphate backbones.

-Justin

> Thank you for any suggestions in advance.
>
> Yang
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--
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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