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.
Thanks again. o. --- On Mon, 6/21/10, Justin A. Lemkul <jalem...@vt.edu> wrote: From: Justin A. Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] Help with defining new residue (OXY--HEME) To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Date: Monday, June 21, 2010, 9:02 AM Omololu Akin-Ojo wrote: > Hi, > > 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? > > I thought of a couple of options: > > 1) Define a new residue -- OXYHEM using the same parameters for HEME as in > ffG43a1.rtp but just adding oxygen--heme interaction. > (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). > ** What are the steps needed to do this? *** > 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. > 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)? > Sure, most things are possible :) See the manual, chapter 5. -Justin > Any help will be appreciated. > > Thanks. > > o. > > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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