Thanks Tsjerk for you reply<br>i did not get your point . i think you are asking me whether i used PBC or not , so i want to tell you that the .tpr file which i used for genion command was created without using PBC. <br><br>
but will it make any difference ? <br><br>Thanks <br>With Regards <br>Gurpreet<br><div><span class="gmail_quote">On 7/16/07, <b class="gmail_sendername">Tsjerk Wassenaar</b> <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com
</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;">Gurpreet,<br><br>> my system was going fine at that time but when i used the genion command to
<br>> add ions , i found that my protein was broken into parts.<br>> what could be the reason for this ?<br><br>PBC?<br><br>> While running the genion it usually asked for the group into which we want<br>> to add the ions so i have checked with both the SOL group and OTH group
<br>> seperatly , in both the cases ions were replacing the solvent molecules. Is<br>> their any way by which we can add ions without replacing any solvent<br>> molecules ?<br><br>No, there's no space to put them.
<br>Well, you could try to squeeze them in here or there manually, and<br>perform energy minimization...<br><br>Cheers,<br><br>Tsjerk<br><br><br>--<br>Tsjerk A. Wassenaar, Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center
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