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<div class="gmail_quote">On Sat, Aug 8, 2009 at 5:09 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
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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 Justin,<br>I used opls and I already tried PRODRG, but it did not help... I <br></blockquote><br></div>
What force field are you trying to use for your simulation?
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<div>I am using OPLS.</div>
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<div class="im"><span id=""></span><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">appreciate if you give the address of the related page of the website?? <br></blockquote><br></div>From the homepage: Downloads -> User Contributions -> Other software
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<div>Ok, Thanks</div>
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<div class="im"><span id=""></span><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">because I really problems to open some parts of the gromacs website. If non of them help, should I use molden myself to find all the entries???<br>
</blockquote><br></div>I don't know what you mean. However you assign parameters must be consistent with the original derivation of the force field. Whether or not you can do that in molden, I don't know.<br><br>
Between PRODRG and the contributed scripts, you should be able to write toplogies for Gromos, OPLS, and AMBER.</blockquote>
<div>ok, I will try, Thanks.</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>-Justin<br><br>
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<div class="im">Thank you very much for any suggestion.<br><br></div>
<div class="im">On Sat, Aug 8, 2009 at 4:56 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br><br><br> Jamie Seyed wrote:<br><br> Dear gmx users,<br> I need some help for generating a itp file for my molecular<br> structure. I am using molden and now I have the xyz and pdb<br> files. I read through mailing list but seems I should provide<br>
itp myself. But I don't know the right way to do that. Is it<br> using molden and find one-by-one bond sand angles and<br> dihedrals... . If I have already the itp file for a part of<br> molecule is it only to add the information of new atoms to the<br>
old itp file?? I will really appreciate it if someone gives me<br> better ideas and more related information to make my itp file.<br> <br><br> Depending on the force field you want to use, there are various<br>
scripts in the User Contributions section of the Gromacs site. The<br> PRODRG server is also useful for generating an initial topology, but<br> the charges and charge groups it assigns are often unsatisfactory<br>
and require manual adjustment.<br><br> -Justin<br><br> Many Thanks in Advance,<br> Jamie<br><br><br> ------------------------------------------------------------------------<br><br> _______________________________________________<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></div> jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> <<a href="http://vt.edu/" target="_blank">http://vt.edu/</a>> | (540) 231-9080
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<div class="h5"><br>-- <br>========================================<br><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>
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