Thank you, Dr. Case.
Looking at chapter 39.4, I assume the script at the end is a nab script
that can be compiled as described in earlier 39.x chapters. Is that
correct?
-Robert Kirk DeLisle
On Thu, Mar 22, 2018 at 6:30 AM, David A Case <david.case.rutgers.edu>
wrote:
> On Wed, Mar 21, 2018, Robert DeLisle wrote:
> >
> > I cannot, however, find any information about how to perform Normal Mode
> > Analysis using Amber without running a full MD simulation first.
> Ideally, I
> > would be able to simply run NMA and write out a trajectory file suitable
> > for input to PCAsuite.
>
> Please see Chapter 39.4, "Second derivatives and normal modes" in the
> Amber 2017 Reference Manual. I'm not sure what mode format PCAsuite
> requires; inside Amber, you can use the "modes" command inside cpptraj
> to carry out some analyses. Of course, modes themselves are already
> (mass-weighted) principal components.
>
> ...hope this helps....dac
>
>
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Received on Thu Mar 22 2018 - 08:00:02 PDT
