|
|||||||||||||||||||||||||||||||||
AMBER Archive (2007)Subject: RE: AMBER: Targetted MD and ptraj analysis
From: Catein Catherine (askamber23_at_hotmail.com)
You may use vmd for this purpose.> Date: Wed, 19 Sep 2007 01:47:19 -0400> From: yildirim_at_pas.rochester.edu> To: amber_at_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_at_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_at_scripps.edu> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
| |||||||||||||||||||||||||||||||||
|