how to get a folded 3D output

[sher ya]

hi,

we are trying to predict the 3D structure of our DNA aptamer, so we entered the sequence in the data input file (as the following), but it appears the output pdb is a linear sequence without any folding, is this expected or do I need to change the configuration to make it fold first (we previously used mfold to get the secondary structure)?

calcEnergy true
DNA A 1 ACCTGG
firstStage 1
lastStage 1
baseInteractionScaleFactor 100
temperature 30.0
contact AllHeavyAtomSterics A FirstResidue LastResidue

[Samuel Flores]

Hi Sherwood,

Sorry I didn't get a notification of your post. Did we talk about this by phone? You would need to specify the base pairs or any NtC's. There is a simple hairpin example in the tutorial guide that can help. We can also discuss again by phone.

Sam