AMBER Archive (2004)

Subject: AMBER: Re: RSM & ptraj

From: bybaker_at_itsa.ucsf.edu
Date: Sun Oct 31 2004 - 12:43:41 CST

('binary' encoding is not supported, stored as-is) Hello, Elijah:

Thank you for correcting my mistake. I use the input as you suggested. It
works perfect. I got the RSMD values from the four runs.

Thank you very much.

Have a good day!

Bo

On Sun, 31 Oct 2004 00:29:23 -0600 Elijah Gregory wrote:

> You need to load in each trajectory with four trajin commands in
> one input file and then issue an rms command. This should calculate
> the rmsd from the first structure of the first run for all four
> trajectories in succession.
>
> What you are doing is taking the first run and calculating the rmsd
> from the first structure in that run, then loading in the second run
> and calculating the rmsd from the first structure of *that* run, etc.
> Obviously the "distance" between the first structure in a run and the
> first structure in a run will be zero.
>
> Try using this input file:
>
> model1-3mdCA-rms.in
>
> trajin model1-3-md1.crd
> trajin model1-3-md2.crd
> trajin model1-3-md2a.crd
> trajin model1-3-md2b.crd
> rms first out model1-3md-backbone.rms @CA time 0.2
> strip :WAT
> go
>
> Hope this helps,
>
> Elijah Gregory
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu