<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Thanks for your help<br>I hope it will work.<br>Regards<br><br><div>--<br>Sonali Dhindwal</div><br><br>--- On <b>Wed, 24/3/10, Justin A. Lemkul <i><jalemkul@vt.edu></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Justin A. Lemkul <jalemkul@vt.edu><br>Subject: Re: [gmx-users] Query regarding toplogy of Manganese ion in protein<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Wednesday, 24 March, 2010, 5:44 PM<br><br><div class="plainMail"><br><br>sonali dhindwal wrote:<br>> Hello,<br>> <br>> I have protein in my protein, for which i want to run MD simulation.<br>> Could you please help me to know how to generate topology file for Manganese and which force field to use, as none of the force field in Gromacs supports Mn
ion.<br><br>Parameterization is considered a very advanced task, and generating good parameters for a transition metal is especially challenging. See here:<br><br><a href="http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species" target="_blank">http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species</a><br><br>Parameters for Mn are available for the AMBER force fields, which can be incorporated into Gromacs with the ffamber ports. The reference for Mn can be found at:<br><br><a href="http://www.pharmacy.manchester.ac.uk/bryce/amber#ion" target="_blank">http://www.pharmacy.manchester.ac.uk/bryce/amber#ion</a><br><br>-Justin<br><br>> Please Help<br>> Regards<br>> <br>> --<br>> Sonali Dhindwal<br>> <br>> <br>> ------------------------------------------------------------------------<br>> Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! <<a
href="http://in.rd.yahoo.com/tagline_ie8_new/*http://downloads.yahoo.com/in/internetexplorer/" target="_blank">http://in.rd.yahoo.com/tagline_ie8_new/*http://downloads.yahoo.com/in/internetexplorer/</a>>. <br>> <br><br>-- ========================================<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]vt.edu | (540) 231-9080<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>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search
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