AMBER Archive (2005)

Subject: Re: AMBER: fit

From: Kateryna Miroshnychenko (kateryna_mirosh_at_ire.kharkov.ua)
Date: Mon Jul 25 2005 - 05:11:11 CDT

Dear Yong,

Try following ptraj.in

trajin your_trajectory_file.mdcrd
trajout coord_20_40.mdcrd
rms first out your.rms :20,21,39,40 time x.x
strip :1-19,41-100

x.x is time interval between to subsequent snapshots of your
trajectory. It is needed if you want to plot rms versus time.

Regards,
Katya

> I want to output the coordinates of residues 20-40 of a protein (100 residues), at the same time I want to do fit acoording
> to residues 20,21, 39 and 40.
> how to write ptraj.in or carnal.in file to do this ?
>
> any suggestin would be highly appreciated!
>
> Yong Xu

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