Hello AMBER Community!
I am hoping to run simulations where a peptide's backbone is constrained to
be alpha helical. If I were to do this by applying restraints (ntr=1), that
would also fix the restrained atoms in space, which I don't want - I want
the peptide to be able to move around in the simulation box, while being
forced to retain its helical conformation (and preferably still allowing
side chains to move normally).
The only way I can think of to accomplish this would be to try to overwrite
the phi/psi backbone dihedral parameters in some way to effectively force
these dihedrals to retain standard values for an alpha helix. Would that be
a possible approach? Are there any better ways to accomplish this?
Any input would be greatly appreciated!
Thanks,
Cianna
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Received on Wed Oct 19 2022 - 21:00:03 PDT
