<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hello All ,<br>
I am also trying to simulate my protein with Mn ion present in it.<br>So can I create the topology entry for Mn ion similar to MG2+ ion ? and how can I get the values of C6 and C12 leonard jones potential in [atom type] entry and will it be required to add [nonbond_params] also ? how can I get them ?<br><br>Also I want to use Fe2+ also, but it is also not included in gromos force field. This problem of adding other ions and molecule in the system always remains. And being new to this field, can someone suggest in simple terms how to include these considering the person is not an expert in this field.<br>Please help.<br><br><div>--<br>Sonali Dhindwal</div><br><br>--- On <b>Tue, 8/6/10, Vitaly Chaban <i><vvchaban@gmail.com></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Vitaly Chaban <vvchaban@gmail.com><br>Subject: [gmx-users] Re: Simulation with
CsCl<br>To: gmx-users@gromacs.org<br>Date: Tuesday, 8 June, 2010, 9:03 PM<br><br><div class="plainMail">> Hi all:<br>> I am trying to simulate a polysaccharide in solution of water and CsCl, but<br>> cesium is not parametrized in the gromacs 4. I am using the force<br>> field GROMOS 96.<br>> I have looked for the parameters of Cs+ in the OPLS Force field and I have<br>> created 4 files: Cs.atp, Cs.itp, Csnb.itp and Cs.rtp. Also I have include<br>> the parameters for Cs+ in the "ions.itp" file, but it didn't work, Can<br>> someone help me?<br>> Thanks in advance.<br>> Cecilia.<br><br>Cecilia -<br><br>You do not need so many files so cesium. Just copy your parameters to<br>the force field used and create the topology entry for cesium similar<br>to<br><br>[ moleculetype ]<br>Ar 1<br><br>[ atoms ]<br>1 Ar 1 Ar Ar
0 0.0<br><br>Do not forget, cesium+ is an ion...<br><br>-- <br>Dr. Vitaly Chaban<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 the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></div></blockquote></td></tr></table><br>