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<br>
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Date: Sat, 10 Sep 2011 00:00:23 +0300<br>
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Hi. I've look through the manual and didn't find an answer on my question:<br>
i've got a trajectory and i want to convert it in *.pdb with such parameters<br>
of index file [all atoms within a sphere with a chosen radius around<br>
selected atom]. What can i do? Thank you<br>
<br>
<br>
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Message: 5<br>
Date: Fri, 09 Sep 2011 17:02:40 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] (no subject)<br>
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Алексей Раевский wrote:<br>
> Hi. I've look through the manual and didn't find an answer on my<br>
> question: i've got a trajectory and i want to convert it in *.pdb with<br>
> such parameters of index file [all atoms within a sphere with a chosen<br>
> radius around selected atom]. What can i do? Thank you<br>
><br>
<br>
Use g_select to generate the index group and trjconv to write the file in the<br>
format (and with the contents) that you want.<br>
<br>
-Justin<br>
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========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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