AMBER Archive (2008)

Subject: RE: AMBER:

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Thu Mar 06 2008 - 12:27:34 CST

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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of Thomas Steinbrecher
Sent: Thursday, March 06, 2008 1:13 PM
To: amber_at_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_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

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