[gmx-users] g_order and the tpr file

[Justin A. Lemkul]

Age.Skjevik at biomed.uib.no wrote:
> 
> Dear GROMACS users,
> 
> I've simulated a membrane system with AMBER 9.0, and now I'm trying to 
> calculate order
> parameters for the carbon atoms in the fatty acid tails with the help of 
> g_order. I've
> converted my AMBER trajectory to gromacs xtc and gro files. How can I 
> obtain the tpr file
> needed as input for g_order?
> 

That will require the generation of a suitable topology; this may or may not 
involve pdb2gmx, depending on if you have a protein present in your system.  If 
you have a pure membrane, you will have to make the topology by hand to include 
the proper .itp files, if you have them.  Chapter 5 of the manual is your friend 
here, as are the various tutorials that are available on the web.

-Justin

> Thanks in advance.
> 
> Best regards,
> 
> Åge A. Skjevik, University of Bergen, Norway
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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