Hi Raja,<br><br>You may be better off just adding bonds. I believe there was a bond type (type 6) which was especially useful (intended?) for keeping metals bound to a protein.<br><br>Cheers,<br><br>Tsjerk<br><br><div><span class="gmail_quote">
On 4/20/06, <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;">
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>[ 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>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>define = -DDISRES<br>disre = Simple<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
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</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>