[gmx-users] adding metal ion

[Smith, Micholas D.]

Adding an individual ion to a protein complex is simple: just open vmd or other visualization/building software, and position the ion where you expect it to be. Run energy minimization and check to make sure the ion is where you expect it to be.  

Now the tricky part is to make sure you have the proper parameters for the ion. With that in mind you should ask yourself, before going any further: 

Is the ion crucial to the behaviour of the system you are studying? If so, does the force-field you are using have the parameters for this ion? If not, you are going to need to find some. If no one has published any parameters, than you are going to need to parameterize the ion in question (selenium) yourself, which can be quite a labor intensive process.

===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Meenakshi Rajput <ashi.rajput39 at gmail.com>
Sent: Monday, March 09, 2015 4:11 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] adding metal ion

hello users
I need to add selenium ion in the protein complex. Can anyone tell me how
to add a metal ion in gromacs? I posted the question before but I didn't
get any reply so I am posting again. Please tell me if anybody knows.
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