Hi Raja,<br><br>Yes, that's the idea. So funct (which is 2 now) is changed to 6, but you will still need to specify the equilibrium bond length and the force constant. The bond length can be chosen from the crystal structure, if no other information is available, and the force constant isn't too important if the purpose is too keep the things together. But there must be some parameters for Fe(II)-ligand bonds lying around somewhere.
<br><br>Cheers,<br><br>Tsjerk<br><br><div><span class="gmail_quote">On 4/25/06, <b class="gmail_sendername">raja</b> <<a href="mailto:raja_28@fastmail.us">raja_28@fastmail.us</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Mr.Tsjerk,<br> Thanks for your reply and I checked manual based on your<br> suggestion. I just want to make it sure, Is it what the manual<br> says while adding type 6 bond that is to edit the protein.top
<br> file under [bond] section so as to depict harmonic interaction<br> between metal and ligating atoms.<br><br>###################################<br>[ bonds ]<br>; ai aj funct c0 c1 c2
<br>c3<br> 4734 3724 2<br> 4734 2839 2<br> 4734 2872 2<br>#####################################<br><br>Where 4734 is Fe(II) atom and 3724,2839,2872 are respective metal<br>chelating atoms of protein.<br><br>Is it ok ?
<br><br>With thanks !<br>B.Nataraj<br><br><br><br>On Thu, 20 Apr 2006 10:11:34 +0200, "Tsjerk Wassenaar"<br><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> said:<br>> Hi Raja,<br>><br>> You may be better off just adding bonds. I believe there was a bond type
<br>> (type 6) which was especially useful (intended?) for keeping metals bound<br>> to<br>> a protein.<br>><br>> Cheers,<br>><br>> Tsjerk<br>><br>> On 4/20/06, raja <<a href="mailto:raja_28@fastmail.us">
raja_28@fastmail.us</a>> wrote:<br>> ><br>> > Dear all,<br>> > My intention is to restrict Fe(II) in active site by distance<br>> > restraint protocol. Fe(II) is ligated by three amino acides' polar
<br>> > atoms respectively by (1) NE2 of HIS ,(2) NE2 of HIS (3) OD1 of<br>> > ASP. The following is the disres itp file I used (copied from<br>> > manual3.3). where I edited the atom number of
<br>> > aminoacids(3724,2839,2872) and Fe(II) as 4734.<br>> > ############################# disres.itp<br>> ><br>> > #############################################################################
<br>> > [ distance restraints ]<br>> > ; ai aj type index type' low up1 up2 fac<br>> > 3724 4734 1 0 1 0.0 2.09 0.4 1.0<br>> > 2839 4734 1 0 1
0.0 2.25 0.4 1.0<br>> > 2872 4734 1 0 1 0.0 2.18 0.4 1.0<br>> ><br>> ><br>> > ########################################################################################################################
<br>> ><br>> > I do not understand the meaning of up2 and fac so I left with 0.4 and<br>> > 1.0 as such as found in manual.<br>> ><br>> > In mdp file I added the following the commands<br>> >
<br>> > ###################### full.mdp<br>> ><br>> > ######################################################################################<br>> ><br>> > define = -DDISRES<br>
> > disre = Simple<br>> ><br>> > #######################################################################################################################<br>> ><br>> > I expected these modifictions will restrict but those distances are not
<br>> > restrainted....why ?<br>> ><br>> > Kindly explain me that wheather I need to change any other parameter .<br>> ><br>> > With thanks !<br>> > B.Nataraj<br>> ><br>> ><br>
> > --<br>> > raja<br>> > <a href="mailto:raja_28@fastmail.us">raja_28@fastmail.us</a><br>> ><br>> > --<br>> > <a href="http://www.fastmail.fm">http://www.fastmail.fm</a> - IMAP accessible web-mail
<br>> ><br>> > _______________________________________________<br>> > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> > Please don't post (un)subscribe requests to the list. Use the<br>> > www interface or send it to <a href="mailto: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">http://www.gromacs.org/mailing_lists/users.php</a><br>> ><br>><br>><br>><br>> --<br>><br>> Tsjerk A. Wassenaar,
M.Sc.<br>> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>> Dept. of Biophysical Chemistry<br>> University of Groningen<br>> Nijenborgh 4<br>> 9747AG Groningen, The Netherlands<br>> +31 50 363 4336
<br>--<br> raja<br> <a href="mailto:raja_28@fastmail.us">raja_28@fastmail.us</a><br><br>--<br><a href="http://www.fastmail.fm">http://www.fastmail.fm</a> - I mean, what is it about a decent email service?<br><br>_______________________________________________
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</a><br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>
Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>