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Hello Valerie--
> I have tried to modify the saWithPreAllNoRdc.py script from the PrePot
> distribution to calculate the structure of a complex using only PRE
> data. I have the PDBs for both proteins. If I use something like
> dyn.fix, it doesn't look like the proteins move in space. So, I am
> currently testing the script with dyn.group in the IVM portion.
yes- you will need this for at least one protein.
> Is
> this the correct approach? Should I use a "vector do" command for
> randomizing velocities?
You can. Or you can use
protocol.initDynamics(...,
initVelocities=True)
>
> These proteins likely form a weak-affinity complex, so I only have PRE
> data (1H Gamma2 values) to model the interaction. Using the dyn.group
> approach, it looks like the secondary structure and tertiary structure
> are being perturbed. Has anyone used this script before for only PDBs
> and PRE data?
If you're using group(), the structure is not being perturbed by the
IVM- however, I believe there are other non-IVM statements in that
script which might mess things up.
I suspect that you've found the script you're working from to be not so
straightforward. I hope to have a rewritten script ready soon.
best regards--
Charles
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