AMBER Archive (2009)

Subject: Re: [AMBER] Circular RNA topology file

From: Filip Lankas (
Date: Mon Oct 26 2009 - 05:13:46 CDT

> Second, be sure to use the "bond" command to add the O-P bond that completes
> the circle. Visualize the result in xleap to be sure that exactly the bonds
> that you want are there. Or, you can load the prmtop file into VMD and that
> can also be used to visualize the bonding.
Yet another possibility is to use the "desc" command in Leap on the
atoms involved in the circle closing. "desc" will print out atoms which
the atom in question is bonded to. See the Leap section of the
AmberTools manual for more info and examples.

Double check that you did actually close the circle, there is nothing
worse than simulating for some time only to find out that you forgot to
close it. You might want to look at our paper about simulating circular DNA:

F Lankas, R Lavery, JH Maddocks (2006): Kinking occurs during molecular
dynamics simulations of small DNA minicircles. Structure 14, 1527-1534


Dr. Filip Lankas
Centre for Complex Molecular Systems and Biomolecules
Institute of Organic Chemistry and Biochemistry
Flemingovo nam. 2
166 10 Praha 6
Czech Republic

Phone: +420 - 220 410 319 Fax: +420 - 220 410 320

Secretary: Helena Cerna, phone +420 - 220 410 321

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