Re: [AMBER] unusual structure after heating. why?

From: Daniel Roe <>
Date: Sat, 24 Jan 2015 16:52:49 -0700


On Sat, Jan 24, 2015 at 12:14 PM, Atila Petrosian
<> wrote:
> Note that rmsd plot before and after autoimaging is the same.

Note that this is expected if calculating the best-fit RMSD of a
single molecule (since it is an internal measure). Problems with
imaging and RMSD etc manifest in systems with 2 or more molecules of
interest, for example a DNA duplex, when 1 strand is imaged and the
other is not.

> Is this rmsd plot normal and usual? If not, please help me to resolve this
> problem.

It could be. It doesn't look to me like an imaging problem, since the
transition is relatively smooth. As Jason said, your best bet is
probably to visualize the trajectory at several of these spots to see
what is going on. You can use cpptraj to extract several frames like

parm comp1_sol.prmtop
trajin autoimaged.mdcrd
trajout frame.rst7 onlyframes 500,1000,1500,2000

Note that the '.rst7' file name extension will automatically select
the Amber restart format.

Hope this helps,


> Best wishes,
> Atila
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sat Jan 24 2015 - 16:00:03 PST
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