AMBER Archive (2009)

Subject: Re: [AMBER] DNA simulation: Problem with RMSD

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Wed Mar 04 2009 - 22:04:53 CST

> I am doing a MD simulation on a 12mer DNA, for all my RMSD ,
> helicoidal analysis i wish to remove the terminal base pairs from the
> analysis. How to go about.

The first question is why you would want to remove the terminal base pairs
as these are an integral part of the structure. Plus, frequent fraying at
the end could be indicative of instability. Regardless, if you want to
remove the terminii you could use the strip command

> trajin traj1.mdcrd
> trajin traj2.mdcrd
> trajout fixed.traj
> rms first out rms :2-11,13-23 time 0.2
> center :1-24
> image
> strip :WAT
> go

OK, first problem with the above is that you are doing a box rotation with
RMS before you are doing imaging. This is incorrect and needs to be
fixed.

trajin traj1.mdcrd
trajout fixed.traj
center :1-12 mass origin
image origin
center :1-24 mass origin
image origin center
rms first out rms :2-11,13-23 time 0.2
strip :WAT
strip :1,12,13,24

--tec3

> ---------------------------------------
> Is the format correct to calculate RMSD. will my fixed.traj output
> file have the terminal base pairs removed.
>
> regards
> dksenthil,
>
> Graduate Student
> MBU,IISc,
> Bangalore,
> India
>
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\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
-/-
/-\ tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A http://www.chpc.utah.edu/~cheatham

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