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

[Justin A. Lemkul]

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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-- 
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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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