[gmx-users] Re: gmx-users Digest, Vol 89, Issue 52

[Алексей Раевский]

mm...sorry for incorrect explanation of the task. I know how to use
index_ndx and g_select, but I don't know whether it is possible to  create
an index group of all atoms in !!sphere!! with a radius of 10 angstrom
around selected "carbon" (for example). Exactly I don't know how and where
to determine a sphere's parameters. As you understand if this sphere
includes SOL molecules (which are flexible and all time will be changing one
to another from outside to the inside of the sphere), so I have to define
not atom numbers of SOL but constant spatial character of the sphere. IS IT
possible? With a use of index file it will look like a new index.ndx, with
[sphere] section and its content, for each frame

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> Date: Sat, 10 Sep 2011 00:00:23 +0300
> From: ??????? ???????? <rayevsky85 at gmail.com>
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> Hi. I've look through the manual and didn't find an answer on my question:
> i've got a trajectory and i want to convert it in *.pdb with such
> parameters
> of index file [all atoms within a sphere with a chosen radius around
> selected atom]. What can i do? Thank you
>
>
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> Message: 5
> Date: Fri, 09 Sep 2011 17:02:40 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] (no subject)
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E6A7EF0.9050303 at vt.edu>
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>
>
> Алексей Раевский wrote:
> > Hi. I've look through the manual and didn't find an answer on my
> > question: i've got a trajectory and i want to convert it in *.pdb with
> > such parameters of index file [all atoms within a sphere with a chosen
> > radius around selected atom]. What can i do? Thank you
> >
>
> Use g_select to generate the index group and trjconv to write the file in
> the
> format (and with the contents) that you want.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>

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*С уважением!


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