AMBER Archive (2006)

Subject: Re: AMBER: rms processing

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Mon Mar 06 2006 - 18:41:37 CST

I use the following ptraj input file for my rmsd calculations and it
works:

----------- ptraj.in ----------------------
trajin md01.mdcrd
trajin md02.mdcrd
rms first out rms_out_sugar :1-8
center :1-8
-------------------------------------------

In the command line, I use the following:

ptraj prmtop <ptraj.in> out

For more info, check out the following tutorial:

http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_eight/index.htm

Good luck,

On Mon, 6 Mar 2006, A D wrote:

> I'm trying to get the RMSd out of some mdcrd files. I'd previously
> gotten it to work with the tutorial but I can't remember exactly how.
> For providing an input file to ptraj I put the commands
>
> trajin X.mdcrd
> rms first mass out X.rms time 0.1
>
> in the X.rms file.
>
> When I run
> AMBERHOME/exe/ptraj /home/X/X/X.parm7 < /home/X/X/X.rms
>
> it gives me some processing output on the screen and then terminates
>
> WARNING in ptraj(): No input trajectories specified (trajin), aborting
>
> the mdcrd and rms files are in the directory I'm working in...
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
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  - http://www.pas.rochester.edu/~yildirim/			-
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