AMBER Archive (2008)

Subject: Re: AMBER:

From: Jianyin Shao (jyshao2004_at_gmail.com)
Date: Thu Mar 06 2008 - 15:24:03 CST

I think ptraj does not allow white spaces in the mask unless the mask is
quoted. However, double quotes are recommended. The single quotes may be
problematic if the atom name contains single quotes, such as O5' in nucleic
acids.

The mask ":1-200,300-400_at_C,N,O" should work fine, with or without the
quotes.
There is a mistake in Dr. Thomas Steinbrecher's suggestion. It should be
"(:1-200 | :300-400) & @C,N,O" with quotes.

Best,

Jianyin Shao

On 3/6/08, Ross Walker <ross_at_rosswalker.co.uk> wrote:
>
> 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
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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>
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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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