Hi, I'm working on a research about structural changes of DNA. When doing the Molecular Dynamics of DNA molecule using AMBER force field ,two strands get separated. why is it? How can I do a simulation without having this problem and without constraint the DNA ?
Hi Kalani,
Did you do that without counter ions?
If so, you need to add them to neutralize your system.
Or run MDS in implicit solvent:
http://ambermd.org/tutorials/basic/tutorial1/section3.htm
http://ambermd.org/tutorials/basic/tutorial1/section4.htm
Hi Yoshinobu,
Yes I did it with counter ions by neutralizing them. But it didn't work.
Hi Kalani
"two strands get separated" what do you exactly mean by this? Could you share the snap of before MD and after MD?
HI thirumal,
here they are. Two complementary strands get separated after MD simulation.
Hi Kalani,
That looks there are two double strands DNA.
You need to remove either one.
Hi yoshinobu,
No there's only one double strand. The light blue one showing the it's original position.
Hi Kalani,
If you are using AMBER, go through the following tutorial:
http://ambermd.org/tutorials/basic/tutorial1/index.htm
Hi,
I would suggest to use amber99sb ff. Do you have any modified nucleic base that is not present in the default ff? If yes, how did you generate the ff for the new nucleic bases? I suggest to use REDS server to create the ff for new systems. Best of luck!
Hi Hedieh,
No I didn't change any of the bases. Thank you for your suggestion. I'll try it.
Hey Kalani,
Let us know if it works. Also use PME for long range electrostatic interactions.
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