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Questions and answers => RNA structures (DSSR) => Topic started by: namazi on June 10, 2015, 12:00:53 pm

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Title: modified RNA
Post by: namazi on June 10, 2015, 12:00:53 pm

Hi. I want to generate the modified RNA that bases are A/U/C/G; but suger is changed. I just access to "gromacs" as a MD package at now; gromacs couldn't recognize this modified RNA. At first i simulate standard RNA with AMBER force field of GROMACS package but I don't know what I should to do later....Can DSSR software accept this job about simulate this modified RNA? please help me.
Best Regards.

Title: Re: modified RNA
Post by: xiangjun on June 10, 2015, 12:08:06 pm

Hi,

Thanks your interest in using DSSR, and posting on the 3DNA Forum.

I do not think I quite get your point. As far as DSSR is concerned, it is an analysis and annotation tool -- no simulation, no prediction, no energetics. Reading through the DSSR User Manual should give you a better idea of what DSSR is about.

Please be *specific* by providing a *concrete* example to illustrate unambiguously what you want to achieve.

Best regards,

Xiang-Jun

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.