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
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Received on Sun Mar 09 2008 - 06:07:17 PDT
