You may use vmd for this purpose.> Date: Wed, 19 Sep 2007 01:47:19 -0400> From: yildirim.pas.rochester.edu> To: amber.scripps.edu> Subject: AMBER: Targetted MD and ptraj analysis> > Dear AMBER users,> > I have the following ptraj script, which is first alligning the structure> on the specified atoms, and then calculating the RMSD for the specified> atoms.> ---- ptraj.in ------------------------------> trajin mdcrd_01.traj.p1.gz> rms first out rms_out :1-16.P,O?',C?'> strip :WAT,Na+> principal :1-16 mass> go> --------------------------------------------> Unfortunately, this does not work. I am trying to analyze a targetted MD> simulation, and wondering if it is possible in ptraj to (1) first> alligning the structure on specified atoms, and then (2) calculating the> rmsd of the chosen atoms. Thanks.> > Best,> -- > Ilyas Yildirim> ---------------------------------------------------------------> = Department of Chemistry - => = University of Rochester - => = Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) => = http://www.pas.rochester.edu/~yildirim/ => ---------------------------------------------------------------> > -----------------------------------------------------------------------> The AMBER Mail Reflector> To post, send mail to amber.scripps.edu> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
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Received on Sun Sep 23 2007 - 06:07:36 PDT
