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: [email protected] [[email protected]] On Behalf
Of Justin A. Lemkul [[email protected]]
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
========================================
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