Hi Tom
Thanks. When I said unsuccessful, I meant ptraj was not selecting the
correct regions (strings). I will review the section in the manual on
"ambmask" and try your examples also.
Thanks for your help,
Steve
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of Thomas Steinbrecher
Sent: Thursday, March 06, 2008 1:13 PM
To: amber.scripps.edu
Subject: Re: AMBER:
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.C,N,O :300-400.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.C,N,O or
(:1-200 & :300-400) & .C,N,O
Regards,
Thomas
Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Mar 09 2008 - 06:07:17 PDT
