AMBER Archive (2009)

Subject: [AMBER] ptraj image

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Tue Dec 08 2009 - 15:37:55 CST

Hi,

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

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
trajin cdsDNAch2.mdcrd
trajin cdsDNAceq.mdcrd
trajin cdsDNAcMD1.mdcrd
trajin cdsDNAcMD2.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

~

Thanks

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