Dear users,<br><br>If I obtain/generate the topology file for a ligand using another program (except PRODRG);<br><br>1) How can I arrange .itp file? Because it seems very complicate.<br>2) Justin tutorial:<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html</a><br>
We will make use of two files that PRODRG gives us. Save the output of the field "The GROMOS87/GROMACS coordinate file (polar/aromatic hydrogens)" into a text file called "jz4.gro" and "The GROMACS topology" into a file called "drg.itp."<br>
Then how can I generate .gro file using another program?<br><br>I was obtaining .gro and .itp files using PRODRG but PRODRG is giving improper results/output.<br><br>best regards<br><br><br><div class="gmail_quote">2011/9/17 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im">On 17/09/2011 11:28 PM, ahmet yıldırım wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Tsjerk and Justin,<br>
<br>
Thanks for your reply. I will contact the PRODRG developers.<br>
can you suggest anyway/anytool for generating ligand coordinates/topologies?<br>
</blockquote>
<br>
</div><a href="http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation" target="_blank">http://www.gromacs.org/<u></u>Documentation/How-tos/Steps_<u></u>to_Perform_a_Simulation</a><br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>