<div>Hi Justin,</div>
<div> </div>
<div>On Tue, Jul 21, 2009 at 5:04 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br></div>
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<div class="im"><br><br>Jamie Seyed wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi,<br>Thanks for your comments. But I do not know how to get (or make) the pdb file if it is not made (let say for a new system). Are you using special software to do that to make a pdb or gro file, before starting the simulation?<br>
</blockquote><br></div>That's going to depend entirely upon what that system is. Building a protein or peptide is not so trivial. Building a small molecule is fairly straightforward using programs like PRODRG (online) or xLeap (part of AmberTools).<br>
<br>That said, if your goal is to simulate some arbitrary small molecules, the previous advice of using pdb2gmx will not apply. You will have to build the topologies yourself. </blockquote>
<div> </div>
<div>Is the result of using these programs a pdb file or gro...... would you please explain a little bit?</div>
<div>The systems that I want to simulate are fullerene and CNT. But before that I will simulate a box of water, spce. In this case is it ok to use spc216.pdb (??) or I should use the programs you mentioned?</div>
<div>Sorry for these simple questions......</div>
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<div class="im"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Another thing: It is not possible for me to open some web-pages that users are referring to (some of them are crucial to get the answer)!! Did you face with the same problem or there is new web-address for them??<br>
<br></blockquote><br></div>If you cite some examples, maybe someone can point you in the right direction. The Gromacs webpage is currently migrating to a new site; old webpages can be accessed by appending "old" to the URL, i.e. <a href="http://oldwww.gromacs.org/" target="_blank">http://oldwww.gromacs.org</a> is the old home page.</blockquote>
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<div>For example I checked <a href="http://www.gromacs.org/WIKI-import/PRODRG">http://www.gromacs.org/WIKI-import/PRODRG</a> as you mentioned, but I can not open links on the page. All of them (check force field for example) can not open with like this message "Site settings could not be loaded"...</div>
<div>Is it the page I should use to get a pdb file for my system?? I really appreciate if you let me know the exact web-address to use PRODRG or xLeap (?).</div>
<div> </div>
<div>Thanks a lot,</div>
<div>Jamie</div>
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<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><span id=""></span><br><br>-Justin<br><br>
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<div class="im">Thanks for your help,<br>Jamie<br><br></div>
<div class="im">On Tue, Jul 21, 2009 at 4:17 PM, Rodrigo faccioli <<a href="mailto:rodrigo_faccioli@uol.com.br" target="_blank">rodrigo_faccioli@uol.com.br</a> <mailto:<a href="mailto:rodrigo_faccioli@uol.com.br" target="_blank">rodrigo_faccioli@uol.com.br</a>>> wrote:<br>
<br> Hi,<br><br> If I understood your question, do you want to know how can you start<br> a simulation? So, if I'm correct I recommend this link<br> <a href="http://www.gromacs.org/WIKI-import/Main_Page/Beginners" target="_blank">http://www.gromacs.org/WIKI-import/Main_Page/Beginners</a> to you. In<br>
this link, there is flowsheet file which is the flowchart to Gromacs<br> simulation.<br><br> Answered your question a little more specific, although basically, after you get the pdb file, you need to run the pdb2gmx program. The<br>
link above explains more details about it.<br><br> I hope that this email helped you.<br><br> Cheers,<br> --<br> Rodrigo Antonio Faccioli<br> Ph.D Student in Electrical Engineering<br> University of Sao Paulo - USP<br>
Engineering School of Sao Carlos - EESC<br> Department of Electrical Engineering - SEL<br> Intelligent System in Structure Bioinformatics<br></div> <a href="http://laips.sel.eesc.usp.br/" target="_blank">http://laips.sel.eesc.usp.br</a> <<a href="http://laips.sel.eesc.usp.br/" target="_blank">http://laips.sel.eesc.usp.br/</a>>
<div class="im"><br> Phone: 55 (16) 3373-9366 Ext 229<br> Curriculum Lattes - <a href="http://lattes.cnpq.br/1025157978990218" target="_blank">http://lattes.cnpq.br/1025157978990218</a><br><br><br> On Tue, Jul 21, 2009 at 4:52 PM, Jamie Seyed <<a href="mailto:jamie.seyed@gmail.com" target="_blank">jamie.seyed@gmail.com</a><br>
</div>
<div class="im"> <mailto:<a href="mailto:jamie.seyed@gmail.com" target="_blank">jamie.seyed@gmail.com</a>>> wrote:<br><br> Hi,<br><br> I have a basic question (since I am new). For starting any<br>
simulation as I understand, is to find a .pdb or .gor file. Pdb<br> files for proteins are already there, but for a new system what<br> is the easiest and quick way to find it (which software etc).<br> What about .gro files?????<br>
<br> <br> I appreciate your help for solve my basic problems.<br><br> Thanks, Jamie<br><br><br> _______________________________________________<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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<br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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