Hi Kirtana,
If you take a look at my previous bug report (please see:
http://archive.ambermd.org/201109/0010.html), you will see originally a
routine called PTRAJ with the vector option can generate those kind of
stuff. You just need to mask out relevant atoms/molecules. More clearly
command you need to use is something like in an trajin file "vector
principal [x|y|z]". But unfortunately, it doesn't calculate them right.
Therefore i strongly advise you to write your own code. It is not so hard as
it sounds. Let me give you a quick method below;
using cpptraj or ptraj mask out all irrelevant atoms. put the frame of
reference of the system to the center. make a pdb file out of snapshot from
trajectory. Then with another program/script calculate inertia axes and
center of mass.
hope this hels
best
peker
On Tue, Sep 6, 2011 at 2:27 PM, John S <s.john634.gmail.com> wrote:
> I am trying to calculate the moment of inertia of my solute.
> Can anyone suggest if AMBER has this tool inbuilt.
> on using analin how can we get the principal moment of inertia x, y,z axes.
>
> thanks
> kirtana
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Received on Tue Sep 06 2011 - 12:00:04 PDT
