simtk.org

Hello,

I am currently using version 2_17_1 for Linux and would like to model DNA G quadruplex structures. I am attempting to use the following base interaction:

baseInteraction A 1 WatsonCrick A 7 Hoogsteen cis

However I am meet with the response:

Unable to find parameters for interaction : baseInteraction between residue type: "DG " , and residue type "DG ", parameter WatsonCrick, Hoogsteenm orientation cis between residue numbers 1 and 7

If you have any solution or recommendations for this problem it would be greatly appreciated.

Thank you,
Juan Canoura

Ack! Sorry I missed this. I was getting ready for my summer teaching, not that that is such a great excuse.

Your first problem is that "Cis" should be capitalized. Sorry MMB is case-sensitive. I have not gotten around to making it case-insensitive.

However the "Cis" thing alone is not enough. I actually created a special SamePolarityQuadStacking3 interaction to get the right stacking between tetrads. I append a snippet below that gives you the idea. Without these, I think you would not get the right stacking.

I actually spent a lot of time doing quadruplex modeling. We also did reasonably extensive MD simulations of both DNA and RNA quadruplexes, and got some interesting parameters. We have been casting around for an excuse to publish these. If you are interested there may be a logical and productive collaboration in this. Actually my collaborator is in Florida.

With kind regards,

Sam

PS are you a spanish speaker?


RNA A 1 GGGGCCGGGGCCGGGGCCGGGGCCGGGGCCGGGGCCGGGGCCGGGGCC
numReportingIntervals 80
reportingInterval .1
temperature 100
forceMultiplier 2000


baseInteraction A 1+24 WatsonCrick A 7+24 Hoogsteen Cis
baseInteraction A 2+24 WatsonCrick A 8+24 Hoogsteen Cis
baseInteraction A 3+24 WatsonCrick A 9+24 Hoogsteen Cis
baseInteraction A 4+24 WatsonCrick A 10+24 Hoogsteen Cis


baseInteraction A 7+24 WatsonCrick A 13+24 Hoogsteen Cis
baseInteraction A 8+24 WatsonCrick A 14+24 Hoogsteen Cis
baseInteraction A 9+24 WatsonCrick A 15+24 Hoogsteen Cis
baseInteraction A 10+24 WatsonCrick A 16+24 Hoogsteen Cis


baseInteraction A 13+24 WatsonCrick A 19+24 Hoogsteen Cis
baseInteraction A 14+24 WatsonCrick A 20+24 Hoogsteen Cis
baseInteraction A 15+24 WatsonCrick A 21+24 Hoogsteen Cis
baseInteraction A 16+24 WatsonCrick A 22+24 Hoogsteen Cis

baseInteraction A 19+24 WatsonCrick A 1+24 Hoogsteen Cis
baseInteraction A 20+24 WatsonCrick A 2+24 Hoogsteen Cis
baseInteraction A 21+24 WatsonCrick A 3+24 Hoogsteen Cis
baseInteraction A 22+24 WatsonCrick A 4+24 Hoogsteen Cis

baseInteraction A 1+24 SamePolarityQuadStacking3 A 2+24 SamePolarityQuadStacking5 Cis
baseInteraction A 2+24 SamePolarityQuadStacking3 A 3+24 SamePolarityQuadStacking5 Cis
baseInteraction A 3+24 SamePolarityQuadStacking3 A 4+24 SamePolarityQuadStacking5 Cis

baseInteraction A 7+24 SamePolarityQuadStacking3 A 8+24 SamePolarityQuadStacking5 Cis
baseInteraction A 8+24 SamePolarityQuadStacking3 A 9+24 SamePolarityQuadStacking5 Cis
baseInteraction A 9+24 SamePolarityQuadStacking3 A 10+24 SamePolarityQuadStacking5 Cis

baseInteraction A 13+24 SamePolarityQuadStacking3 A 14+24 SamePolarityQuadStacking5 Cis
baseInteraction A 14+24 SamePolarityQuadStacking3 A 15+24 SamePolarityQuadStacking5 Cis
baseInteraction A 15+24 SamePolarityQuadStacking3 A 16+24 SamePolarityQuadStacking5 Cis

baseInteraction A 19+24 SamePolarityQuadStacking3 A 20+24 SamePolarityQuadStacking5 Cis
baseInteraction A 20+24 SamePolarityQuadStacking3 A 21+24 SamePolarityQuadStacking5 Cis
baseInteraction A 21+24 SamePolarityQuadStacking3 A 22+24 SamePolarityQuadStacking5 Cis