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Re: where can I find the parameters about GC pair
ckc1117 #18539 08/02/08 03:28 AM
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I mean that the phosphodeoxyribose backbone and additional base pairs are needed to get stable H-bonds. Experimentally, most biological helices require a couple turns of the helix in order to be stable in aqueous solution.

Re: where can I find the parameters about GC pair
rmv #18540 08/03/08 02:59 AM
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I see others's work (year 1997) using CHARMM23 parameter doing MD of the GC pair are quite stable , after MD simulation, the two bases are in a plane, but in my case, during 1ns equilibrium step, the G-C pair flying apart though they are H-bonded in the first 250ps. is it something to do with the initial sturcture ? and is it any way to make them more stable in a plane ?
thank you very much !

Re: where can I find the parameters about GC pair
ckc1117 #18541 08/03/08 05:34 PM
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Perhaps there are some differences between your setup and what was used in the paper; you'll have to look into that more carefully.

I do not recommend using restraints to impose your expectation of what the results should be; that's known as biasing the results.

Re: where can I find the parameters about GC pair
rmv #18542 08/04/08 12:57 PM
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you are right, I shall take more respect of the results.
in the paper mentioned above, they didn't mention the solvation box, they should just do it only with base pairs.
but what shall I do with my simulation of G-C pair in water box, it seems all right that the bases fly apart or they form stacking but not pair during equilibrium step. but I can't perform vibrational analysis to check the H-bond effect on the sturcture.
but is it still meaningful go on the simulation and check the sturctural fluctuation?
and by the way, is there any already published paper about base pair simulation ? I didn't find about G-C pair yet.
thank you for your time !

Last edited by ckc1117; 08/04/08 12:58 PM.
Re: where can I find the parameters about GC pair
ckc1117 #18543 08/04/08 04:47 PM
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It has been said that six months of effort (lab experiments, or modeling and computer time) can save you a day in the library.

Are there any experimental papers that suggest the isolated G and C free bases form long lasting H-bonded stable complexes in aqueous solution?

I should note perhaps a new post (after some library research on your part) in another forum may be called for; this is no longer about G, C parameters ...

Re: where can I find the parameters about GC pair
rmv #18544 08/05/08 01:24 AM
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I am really rush into these works, and did not take enough time to do the research. it is really not good.
thank you for reminding me sir!

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