AMBER Archive (2009)

Subject: Re: [AMBER] ptraj image

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Tue Dec 08 2009 - 15:50:09 CST

> i am having difficulty getting a double stranded DNA to appear in one
> orientation in vmd

I have had this problem myself...

> i use the following script in ptraj. in the manual it is recommended to
> use image :1-38 bymask :1-38 and image origin center familiar. both of
> these commands separated the double strands in vmd. the only script that
> kept the double strands together and centered is below. however the
> orientation of the dsDNA between the files changes making the movie
> unpleasant to watch. any suggestions?
>
> trajin cdsDNAch1.mdcrd
> trajout cdsDNAc.mdcrd
> reference cdsDNAcmn2.rst
> rms reference mass out DNA.dat ':1-38' time 10
> rms reference out Naion.dat ':39-74' time 10
> strip :WAT*
> center :1-38
> go

You have no imaging commands? If the box is small relative to the
biomolecule, imaging of multiple molecules can be tricky. I often try
centering the first residue (:1) imaging, and then centering every thing
and imaging again.

If the box is big enough, you should be able to center the first strand,
image, center both strands, image and be OK.

All the center/image should happen prior to the RMS fit since this rotates
things...

--tec3

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