Never mind - I had been looking for the wrong kind of trick: It seems I
don't need to modify the prmtop or load different parameters, just to apply
dihedral restraints with nmropt. Lesson learned!
On Wed, Oct 19, 2022 at 8:49 PM Cianna Calia <ccalia.ucsd.edu> wrote:
> 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 Thu Oct 20 2022 - 01:30:04 PDT
