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Initial Coordinates for ss-DNA
#891 02/04/04 06:08 PM
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In my work with DNA simulations I have taken coordinates from .crd files, and I have used IC SEED & IC BUILD. But I have noticed that when I build ss-DNA using the later method that the initial configuration is fully extended and wonder about the following: Under what time scale can I expect a ss-DNA in explict solvent with 1M excess NaCl to come to a realistic configuration? It just occurred to me as I was posting this that I could run MC before MD, is this best or is there another way for getting good starting coordinates for a ss-DNA that is not in the databanks?

Much Thanks,
Jim


Molecular Engineering Laboratory University of Washington
Re: Initial Coordinates for ss-DNA
jimpsull #892 02/04/04 07:54 PM
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It takes quite some time (hundreds of ps) just to loose memory of the starting configuration. You may want to look at this paper:
Sen, S. and L. Nilsson (2001). "MD Simulations of Homomorphous PNA, DNA and RNA Single Strands: Characterization and Comparison of Conformations and Dynamics." J Am Chem Soc 123: 7414-7422.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Initial Coordinates for ss-DNA
lennart #893 02/10/04 09:22 PM
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Thank you. I read your article. In your article, you state "We first generated the atomic coordinates of the single-stranded DNA in B-form..." You mentioned having used Insight II. I am using the academic version of CHARMM (27b4 & 30b1). I would like to know if there are CHARMM scripts available to build coordinates in B-form, A-form, Z-form, etc. given an arbirtrary sequence. When I use IC SEED & IC BUILD I get a fully extended, non-helical form.

Thanks again,

Jim


Molecular Engineering Laboratory University of Washington
Re: Initial Coordinates for ss-DNA
jimpsull #894 02/13/04 11:46 AM
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You could try the program NAB from Dave Case's group:
www.scripps.edu/case


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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