AMBER Archive (2006)

Subject: AMBER: Fw: RMSd calculations

From: Claire Zerafa (cporteli_at_waldonet.net.mt)
Date: Fri May 19 2006 - 07:07:30 CDT

----- Original Message -----
From: Claire Zerafa
To: 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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