<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><div id="yiv1434033614">Thanks, Justin. I appreciate this. I will go with the first option of creating a *.rtp file and manually change the subsequent *.top file to put in the morse potential.<br><br>Thanks again.<br><br>o.<br><br>--- On <b>Mon, 6/21/10, 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] Help with defining new residue (OXY--HEME)<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Monday, June 21, 2010, 9:02 AM<br><br><div class="plainMail"><br><br>Omololu Akin-Ojo wrote:<br>> Hi,<br>> <br>> I obtained parameters for a Morse potential between Oxygen molecule and Iron in heme (from ab initio calculations). How can I
use this potential with the GROMOS96
parameters?<br>> <br>> I thought of a couple of options:<br>> <br>> 1) Define a new residue -- OXYHEM using the same parameters for HEME as in ffG43a1.rtp but just adding oxygen--heme interaction.<br>> (The problem with this is that the bonded interaction in the HEME uses the G96BOND, so, how would I maintain this G96BOND for all the atoms except the oxygen-Fe interaction for which I need to use the Morse potential).<br>> ** What are the steps needed to do this? ***<br>> <br><br>You could create an .rtp entry for this species and process it with pdb2gmx. I don't know how to put a Morse type bond in an .rtp file, but you can easily modify the resulting topology to include the proper term.<br><br>> 2. Is it possible to simply create an appropriate *.itp file to use in conjunction with the HEME already defined in the GROMOS96 files (*.atp, *.itp, *.rtp in /usr/local/gromacs/share/gromacs/top)?<br>> <br><br>Sure, most things
are possible :) See the manual, chapter 5.<br><br>-Justin<br><br>> Any help will be appreciated.<br>> <br>> Thanks.<br>> <br>> o.<br>> <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 rel="nofollow" target="_blank" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- gmx-users mailing list <a rel="nofollow">gmx-users@gromacs.org</a><br><a rel="nofollow" target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a rel="nofollow" target="_blank"
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