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On 23/09/2011 4:48 PM, ahmet yıldırım wrote:
<blockquote
cite="mid:CAKVtM2uCFjJt7S14Or515cpb8NxPxOeSJzOzNd3sKxEtVaProw@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
Yes, this is not an easy thing to do. Modelling an arbitrary organic
compound is a difficult task. There are links from the link I
provided last time that will help you.<br>
<br>
<blockquote
cite="mid:CAKVtM2uCFjJt7S14Or515cpb8NxPxOeSJzOzNd3sKxEtVaProw@mail.gmail.com"
type="cite">2) Justin tutorial:<a moz-do-not-send="true"
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>
</blockquote>
<br>
Again, follow the links, please.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAKVtM2uCFjJt7S14Or515cpb8NxPxOeSJzOzNd3sKxEtVaProw@mail.gmail.com"
type="cite"><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
moz-do-not-send="true" 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 moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation"
target="_blank">http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation</a><br>
<font color="#888888">
<br>
Mark</font>
<div>
<div class="h5"><br>
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</blockquote>
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<br>
-- <br>
Ahmet YILDIRIM<br>
<br>
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