AMBER Archive (2006)

Subject: Re: AMBER: rms processing

From: Jianyin Shao (jyshao2004_at_gmail.com)
Date: Mon Mar 20 2006 - 16:19:25 CST

Hi,

It looks that the problem is trajin, not the rms processing. Please double
check that the mdcrd file is under your working directory. And it looks
X.rms is your input file for ptraj and you designate the output of rms
processing to X.rms too. That may also cause some conflicts or erase your
original X.rms thus not trajin command? Hope it helps.

Jianyin Shao

On 3/6/06, A D <nkomli_at_gmail.com> 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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