Hi Andrea and Liu,<br>
Since you are discussing this topic, I have a general Question.<br>
1.) What is the protein you are using( any ID of the protein to search in protein data bank), and<br>
2) what kind of membrane is it?(DPPC, DOPC??)<br>
And how big is your initial membrane(128 , 256 or 512 lipids??).<br>Thanks in advance,<br>
Viswam.<br>
<br><div><span class="gmail_quote">On 12/15/05, <b class="gmail_sendername">andrea spitaleri</b> <<a href="mailto:spitaleri.andrea@hsr.it">spitaleri.andrea@hsr.it</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 Liu,<br>
I explain it a bit better. Basicaly I create my system
protein/membrane with vmd, not taking in account possible clashes.
Afterwards, I use the gromacs tools, genbox, in order to solvate the
protein with the membrane as well described here:<br>
<a href="http://www.dddc.ac.cn/embo04/practicals/9_16.htm" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://www.dddc.ac.cn/embo04/practicals/9_16.htm</a><br>
genbox remove in such way eventual clashes.<br>
<br>
I hope this is a bit clearer<br>
<br>
Regards<br><span class="sg">
<br>
andrea</span><div><span class="e" id="q_1082ea9cc68a224c_2"><br>
<br>
<div>-- <br>
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Dulbecco Telethon Institute<br>
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Biomolecular NMR, 1B4<br>
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