<div dir="ltr">What I do is visualize as trace. Than all the coarse-grained sphere are connected. Hope it helps. Omer.<br clear="all"> <br>Koby Levy research group,<br>Weizmann Institute of Science. <br>FAX: 972-77-444-7905<br>
<a href="http://www.weizmann.ac.il/sb/faculty_pages/Levy/">http://www.weizmann.ac.il/sb/faculty_pages/Levy/</a><br><br><br>
<div class="gmail_quote">On Fri, Oct 16, 2009 at 11:24, Thomas Schmidt <span dir="ltr"><<a href="mailto:schmidt@bit.uni-bonn.de">schmidt@bit.uni-bonn.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Dear all,<br><br>is there any possibility to give the bond information out of GROMACS<br>files to VMD? Especially for coarse-grained models (using the MARTINI<br>
FF) this would be a nice feature for visualization.<br><br>But in that case the distance analysis doesn't work, because we will<br>always have too high distances between two particles (CG scale). If I<br>use "Dynamic Bonds" (as described in this thread:<br>
<a href="http://oldwww.gromacs.org/pipermail/gmx-users/2008-September/036124.html" target="_blank">http://oldwww.gromacs.org/pipermail/gmx-users/2008-September/036124.html</a>) VMD draws bonds also between non-bonded particles.<br>
<br>I know that there is no official solutions for this<br>(<a href="http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD" target="_blank">http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD</a>), but maybe<br>
anybody of you has a script to convert *.top/*.itp/*.rtp files with a<br>corresponding *.gro file into the PDB format with connectivity section<br>or into the (NAMD) *.psf format. (?)<br>The solution that I've found (<a href="http://top2psd.pl/" target="_blank">top2psd.pl</a>) is not smart enough because<br>
it's a simple 1-to-1 conversion of GROMACS topology files and has not<br>the ability to replicate (and renumber) the topological data of single<br>molecules (<a href="http://baaden.free.fr/soft/compchem.html" target="_blank">http://baaden.free.fr/soft/compchem.html</a>).<br>
<br>Thanks for your help...<br>Thomas<br><br>--<br>Thomas H. Schmidt, PhD student<br>Computational Structural Biology<br>Chair of Life Science Informatics, B-IT<br>LIMES-Institute, University of Bonn<br>Dahlmannstrasse 2, D-53113 Bonn, Germany<br>
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