[gmx-users] NOE distance restraints

Chiara Parravicini parravicini.chiara at gmail.com
Thu Nov 22 11:34:09 CET 2007

Dear Gromacs users,

I intend to perform a MD simulation of a GPCR model applying distant
restraints to the backbone of alpha helices, something like NOE
distance restraints. I guess that gromacs can't do it directly but if
I've well understand I can manually provide classical distance
restraints instead of NOE. My matter is that my model is based on a
X-Ray structure and I've not experience in NMR, so I feel unsure about
the idea.
I've three questions:
Does anybody know if there is a dataset of standard or statistical
distance restraints for typical secondary structures to use as a
template (I need to fix Hbonds between helical turns)?
Or should I better define arbitrary distances assuming a Hbond cutoff?
Given that the NMR structure of my template has been published but is
firmly worse than the X-Ray one, should I looking for experimental
data about it?

Thanks in advance


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