normal Dihedral restraints

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7 years 10 months ago #5586 by beenish
Dihedral restraints was created by beenish
Hi there
I have a horse shoe shaped peptide and I want to conserve its structure which is beta strand coil beta strand. I tried everything starting from conserving sec. structure, elnedyn, creating harmonic bonds (by using distance restraints) between opposite strands. But nothing seems to work. After running the simulation for a very short time the peptide starts to twist and can not maintain its shape. Any idea how I can do it? Should I use dihedral restraints to conserve the backbone dihedrals?
Thanks in advance

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7 years 8 months ago #5725 by bart
Replied by bart on topic Dihedral restraints
Hello,

Depending on the strength of your elastic network the protein should be able to deviate from its reference structure. To understand why your protein has problems to maintain its tertiary structure I would need some more information. Could you tell me more about the procedure you follow to reach your production run?

Cheers,

Bart

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7 years 8 months ago #5726 by beenish
Replied by beenish on topic Dihedral restraints
Hi Bart
I managed to do it with distance restraints.
Thanks,
Beenish

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