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

[Justin A. Lemkul]

He, Yang wrote:
> 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.
> 

The interactions holding DNA together are largely electrostatic.  Aromatic 
stacking also plays a role, but the hydrogen bonding is very important.  That's 
why I think a simple "one particle per base" is not going to be very accurate. 
You can't rely on simply van der Waals interactions alone to hold DNA together.

If others have done simulations successfully with this model, then perhaps speak 
with authors about how they made it work (i.e., the parameters that one would 
specify in a .mdp file or any special nuances of the functional form).

-Justin

> 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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-- 
========================================

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

========================================