Messages

1

General discussions (Q&As) / ideal values for the stacking parameters

« on: October 07, 2008, 04:12:21 pm »

Hi,

we have performed a MD simulation of a DNA duplex and have accumulated a series of snapshots. We'd like to understand how the structure of the duplex is changing during the MD. For this, we want to compare the structure for the snapshots to the structure of an ideal duplex, understanding for an ideal duplex one with a uniform structure.

Then,  assuming there are ideal values for the parameters shift, slide, rise, tilt, roll and twist, we want to see how these parameters change during the MD, as compared to their ideal values.

Now, the question is, are there ideal values for these parameters?

For example, is it reasonable to assume that the ideal values for roll, slide, twist and rise are 0, 0, 36 and 3.4, respectively.

What about shift and tilt, is it reasonable to assume that their ideal values are zero?

Thanks
Miguel

2

General discussions (Q&As) / Re: problems with stacking parameters of a MD-history

« on: March 07, 2008, 03:53:37 pm »

Xiang-Jun,

thanks.

We are analyzing a short ds DNA segment from MD simulations. The
sequence is this:
A1-T10
A2-T9
A3-T8
A4-T7
A5-T6

For some frames, the base pairs in the two ends (i.e. A1-T10, or A5-T6)
are broken and find_pair cannot find them. Therefore only information
for A2-T9, A3-T8, and A4-T7 are output. For example, the rise between
A1-T10 and A2-T9 is not printed out.

We modified some of the max allowed values in the parameters in misc_3dna.par
and redo the analysis. For example, we changed the H-bonding criterion. We have
found that if the criterion value is increased just a little, find_pair still
can not find the broken basepairs in the end. But if it's increased too
much, find_pair will find some unreasonable pairs, such as A5-T7 etc.

The problem above could be solved by finding out the "optimized H-bonding
criterion" for this particular frame, so reasonable base-pairs are found. However,
this optimized value is likely to change when one is analyzing another frame.

Thanks
Miguel

3

General discussions (Q&As) / problems with stacking parameters of a MD-history

« on: March 06, 2008, 01:26:19 pm »

We're using X3DNA to analyze a MD-history of a DNA molecule.

When analyzing the data, we've noticed that for some frames, X3DNA does not
print out parameters. We're specially interested in the parameters that describe
stacked base-pairs (e.g. rise, twist, etc.)

We suspect that X3DNA does not print out parameters such as rise when the
corresponding frame contains stacked base-pairs that are too far from each other.
This is similar to the problem mentioned in Q6 of FAQ, which is related to
H-bonding. Q6 is solved by changing the H-bonding criterion in the file misc_3dna.par

Is it possible to change the default value of rise  so as to allow measuring the
rise of stacked bp that are further than usual? (Is it possible to do something similar for
tilt, role, twist, etc.)

Thanks
Miguel

4

General discussions (Q&As) / h-twist vs. twist

« on: October 05, 2006, 09:32:08 am »

h-twist vs. twist

when running X3DNA the files bp_helical.par and bp_step.par are created. The latter contains
the parameter twist, and the former the parameter h-twist. What does h-twist stand for? helical-twist?
What is the difference between h-twist and twist?

We're working on artificial and natural DNAs and would like to plot an MD-average of the twist
parameter for these duplexes. However, we're not sure whether to plot h-twist or twist.

thanks