AMBER Archive (2008)

Subject: Re: AMBER:

From: Thomas Steinbrecher (
Date: Thu Mar 06 2008 - 12:13:23 CST

Hi Steve,

On Thu, 6 Mar 2008, Steve Seibold wrote:

> Hi Amber
> I am trying to obtain an rms from separate regions of my protein. That
> is I want to leave out a center fragment of the protein for my analysis.
> I have tried the following and derivations of the following, but have
> been unsuccessful.

You dont tell us what unsuccesful means, do you get a segfault, error
message, wrong rms...?

> Trajin file.mdcrd
> Reference fileref.pdb
> Rms reference out file.txt time 5 :1-200_at_C,N,O :300-400_at_C,N,O

You define two separate groups from 1-200 and from 300-400. The ambmask
section of the manual has information on how to combine selection strings.
On the top of my head I would try something like :1-200,300-400_at_C,N,O or
(:1-200 & :300-400) & @C,N,O



Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA

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