Hello Viswanadham and Andrea,<br><br>My protein is generated from our lab, I use dppc128 membrane.<br><br>After I use genbox to remove clashes, I use genbox again to solvate my lipid/protein system in water, but when I do grompp there comes another error:
<br>##########################################################################<br>Fatal error: number of coordinates in coordinate file (merge.gro, 115120) does not match topology (merge.top, 116570)<br>##########################################################################
<br><div><span class="gmail_quote">I download the dppc128 top file from the websit, and generate the protein top file by hand, then I make them as a whole top file for my lipid/protein system, cause there's a error when I use pdb2gmx to generate a top file for the whole system.
<br>If I choose to use the download top file for my bilayer, how can I solve this problem?<br><br>Thanks in advance!<br><br>On 12/15/05, <b class="gmail_sendername">Viswanadham Sridhara</b> <<a href="mailto:muta.mestri@gmail.com">
muta.mestri@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;">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="q"><span class="gmail_quote">On 12/15/05, <b class="gmail_sendername">andrea spitaleri</b> <<a href="mailto:spitaleri.andrea@hsr.it" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
spitaleri.andrea@hsr.it</a>> wrote:</span></span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><span class="e" id="q_1082eb6d85f3cfe1_3">
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>
<br>
andrea</span></span></div><div><span><div><span class="e" id="q_1082eb6d85f3cfe1_5"><br>
<br>
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Dulbecco Telethon Institute<br>
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Biomolecular NMR, 1B4<br>
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20132 Milano (Italy)<br>
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</span></div><span class="q"><br>_______________________________________________<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
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gmx-users-request@gromacs.org</a>.<br><br></span></blockquote></div><span class="sg"><br><br clear="all"><br>-- <br>Viswanadham Sridhara,<br>Graduate Research Assistant,<br>Old Dominion University, "VIRGINIA".<br>
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