AMBER Archive (2003)

Subject: RE: AMBER: RMSD and Radius of Gyration

From: Yong Duan (yduan_at_udel.edu)
Date: Sat Oct 25 2003 - 20:40:07 CDT

As I recall carnal does it and I think ptraj does it too.

yong

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of Carlos Simmerling
Sent: Saturday, October 25, 2003 7:28 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: RMSD and Radius of Gyration

Robert,
my program moil-view calculates radius of gyration
but only runs on SGI- I can't recall is you have an SGI
or not. I'm not sure if ptraj does it, seems like it should.
Maybe Tom will reply.
Carlos

----- Original Message -----
From: "Endres, Robert G." <endresrg_at_ornl.gov>
To: <amber_at_scripps.edu>
Sent: Saturday, October 25, 2003 6:24 PM
Subject: AMBER: RMSD and Radius of Gyration

>
> Dear AMBER users,
> what's the best way to calculate the radius of gyration (moment of
inertia) with amber?
>
> Also, comparing rmsd plots from Ptraj with the movie of same
trajectory,
> I cannot recognize very much correlation between between "good
structures"
> by inspection from movie and smallness of the rmsd value. Does anyone
know
how the fit to a reference structure in ptraj is done? This optimization
procedure
> seems to me highly nontrivial.
>
> Thanks for any suggestions,
>
> Best regards,
> Robert
>
>
>
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