[AMBER] RMSD vs reference substructure

From: Kasprzak, Wojciech (NIH/NCI) [C] <"Kasprzak,>
Date: Tue, 9 Nov 2010 09:29:19 -0500

Dear Amber Users,

I am attempting to compare results of a coarse-grained simulation
with three atoms per nucleotide (RNA) to an all atom MD trajectory.
The full structure has 8460 RNA atoms while the coarse-grained subset
of it has 792. I have attempted to use ptraj rms command, using
selected coarse-grained structures (pdb format, 792 atoms listed in the file)
as references and applying a mask corresponding to the 792 atoms from
the reference structure to all the frames of the Amber MD trajectory.
The ptraj input file looks as follows:

trajin trajectory-without-solvent.x
reference coarse-grained-structure.pdb
rms reference rmsd-output-file.dat .P,C4',C2

The trajectory-without-solvent has been extracted earlier from the solvent box
and properly centered and imaged.

The ptraj command is called with the topology parameters file corresponding
to a pure RNA 8460 at structure (from leap). Ptraj issues expected warnings
for the coarse-grained-structure.pdb input (WARNING: The actual number of
atoms (792) does not match the expected number of atoms (8460)...)
The mask is verified to represent 792 atoms. The programs runs, but the
RMSD values it outputs are almost an order of magnitude larger than the quick
checks I did for individual frames via interactive programs (such as PyMOL).

I can understand the warnings, but I thought it is possible to use an incomplete
reference structure. Am I attempting to do something impossible? If not,
what is the correct way of doing it?

Hoping to get things right, Voytek Kasprzak

Wojciech (Voytek) Kasprzak [Contractor]
Analyst Programmer,
Basic Science Program, SAIC-Frederick, Inc.
National Cancer Institute in Frederick, Frederick, MD
(301) 846 5537
AMBER mailing list
Received on Tue Nov 09 2010 - 07:00:11 PST
Custom Search