AMBER Archive (2006)

Subject: Re: AMBER: Fw: RMSd calculations

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Fri May 19 2006 - 08:00:50 CDT

what is that line after the rmsd command doing (starting with @CA)?
is there line break that should be there?

it might help to tell us if ptraj gave any error messages. did you
look at the ptraj output line by line? it tells you what it is doing.
based on that it is usually easy to find the problem.
Claire Zerafa wrote:

>
> ----- Original Message -----
> *From:* Claire Zerafa <mailto:cporteli_at_waldonet.net.mt>
> *To:* amber_at_scripps.edu <mailto:amber_at_scripps.edu>
> *Sent:* Thursday, May 18, 2006 9:25 PM
> *Subject:* RMSd calculations
>
> Hi amber users,
>
> I am analysing a trajectory spanning 1860ps divided into 11 stages. My
> input ptraj script to calculate RMSd is as shown below, and it worked
> fine when I worked with a first equilibrium 20ps run. When I run this
> script, I only get RMSd values for 479.6 out of the 1860ps
> trajectory, and when I tried to run a similar script with a similar
> trajectory with the same time span the RMSd values got dumped over
> 720ps. Can anyone tell me why this happens please?
>
> Thanks
>
> Claire
>
> undocked_calc_backbone_rms.in
> > trajin /DATA/UNDOCKED_DYNAMICS/1e3g_wat_md2.mdcrd.gz
> > trajin /DATA/UNDOCKED_DYNAMICS/1e3g_wat_md3.mdcrd.gz
> > trajin /DATA/UNDOCKED_DYNAMICS/1e3g_wat_md4.mdcrd.gz
> > trajin /DATA/UNDOCKED_DYNAMICS/1e3g_wat_md5a.mdcrd.gz
> > trajin /DATA/UNDOCKED_DYNAMICS/1e3g_wat_md6.mdcrd.gz
> > trajin /DATA/UNDOCKED_DYNAMICS/1e3g_wat_md7.mdcrd.gz
> > trajin /DATA/UNDOCKED_DYNAMICS/1e3g_wat_md8.mdcrd.gz
> > trajin /DATA/UNDOCKED_DYNAMICS/1e3g_wat_md9.mdcrd.gz
> > trajin /DATA/UNDOCKED_DYNAMICS/1e3g_wat_md10.mdcrd.gz
> > trajin /DATA/UNDOCKED_DYNAMICS/1e3g_wat_md11.mdcrd.gz
> > rms first out /DATA/UNDOCKED_TRAJECTORY_ANALYSIS/undocked_backbone.rms
> > @CA time 0.2
> > strip :WAT
> > go

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