AMBER Archive (2008)

Subject: RE: AMBER:

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Mar 06 2008 - 12:37:16 CST

Hi Steve,

You may need to put quotes around the mask for ptraj to interpret it
correctly.

I.e.

Rms reference out file.txt time 5 ':1-200,300-400_at_C,N,O'

The above mask may still need some tweaking though as I didn't lookup the
actual syntax to be sure.

All the best
Ross

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Steve Seibold
> Sent: Thursday, March 06, 2008 10:28
> To: amber_at_scripps.edu
> Subject: RE: AMBER:
>
> 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
>
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