<div>Hi All, </div>
<div> </div>
<div>I am a newbie to GROMACS, so pardon me if I am wrong. </div>
<div> </div>
<div>I think pdb2gmx can handle this with amber forcefields. We just need to use the right nomenclature. I think the .hdb files for amber ff in GROMACS are already equipped with the necessary info. </div>
<div> </div>
<div>I am not sure why one must use an external software for adding the hydrogen atoms. </div>
<div> </div>
<div>If I am wrong, pls correct me. </div>
<div> </div>
<div>Thank you, </div>
<div>Vignesh<br><br></div>
<div class="gmail_quote">On Fri, May 2, 2008 at 12:09 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br>In terms of external software, check out OpenBabel:<br><a href="http://openbabel.org/wiki/Main_Page" target="_blank">http://openbabel.org/wiki/Main_Page</a><br>
<br>There's also the H++ server, which employs Babel as part of its algorithm:<br><a href="http://biophysics.cs.vt.edu/H++/index.php" target="_blank">http://biophysics.cs.vt.edu/H++/index.php</a><br><br>I believe H++ can handle nucleic acids. You could also do all of this with<br>
Gromacs, if you can come up with relevant entries in the .hdb file for your<br>particular force field. Then pdb2gmx could produce the right structure with<br>added hydrogens.<br><br>-Justin<br>
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<div></div>
<div class="Wj3C7c"><br>Quoting Arijit Maitra <<a href="mailto:arijitmaitra@yahoo.com">arijitmaitra@yahoo.com</a>>:<br><br>> Hi All<br>><br>> I have been trying to simulate a DNA tetramer<br>> d(GGGGTTTTGGGG)_2 using gromacs with amber ports. I<br>
> have downloaded the X-ray structure from<br>> <a href="http://www.rcsb.org/pdb" target="_blank">www.rcsb.org/pdb</a> which has several missing hydrogen<br>> atoms. Can anybody advise how to plug in the missing<br>
> atoms, e.g. with softwares or otherwise to proceed<br>> with the pdb2gmx command?<br>><br>> Thanks<br>> Ari<br>><br>><br>><br>><br>____________________________________________________________________________________<br>
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<br>Justin A. Lemkul<br>Graduate Research Assistant<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br><a href="mailto:jalemkul@vt.edu">jalemkul@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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<div class="Wj3C7c">_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
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<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></div></div></blockquote></div><br><br clear="all"><br>-- <br>R.Vigneshwar<br>
Graduate Student,<br>Dept. of Chemical & Biomolecular Engg,<br>National University of Singapore,<br>Singapore<br><br>"Strive for Excellence, Never be satisfied with the second Best!!"<br><br>"The rewards of sincere resolves are highs money can never buy!"