<div>Hi Justin,</div>
<div>I used opls and I already tried PRODRG, but it did not help... I appreciate if you give the address of the related page of the website?? 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???</div>
<div>Thank you very much for any suggestion.<br><br></div>
<div class="gmail_quote">On Sat, Aug 8, 2009 at 4:56 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<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">Dear gmx users,<br>I need some help for generating a itp file for my molecular structure. I am using molden and now I have the xyz and pdb files. I read through mailing list but seems I should provide itp myself. But I don't know the right way to do that. Is it using molden and find one-by-one bond sand angles and dihedrals... . If I have already the itp file for a part of molecule is it only to add the information of new atoms to the old itp file?? I will really appreciate it if someone gives me better ideas and more related information to make my itp file.<br>
<br></blockquote><br></div>Depending on the force field you want to use, there are various scripts in the User Contributions section of the Gromacs site. The PRODRG server is also useful for generating an initial topology, but the charges and charge groups it assigns are often unsatisfactory and require manual adjustment.<br>
<br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im">Many Thanks in Advance,<br>Jamie<br><br><br></div>------------------------------------------------------------------------<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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</blockquote><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>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>_______________________________________________<br>
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Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
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