Dear Gromacs users...<br><br>I am new to gromacs...<br><br>I have not understood this <br><br>"<p>In your shell configuration file (e.g. <span style="font-family:courier new,courier,monospace">.bashrc</span> for <span style="font-family:courier new,courier,monospace">bash</span> or <span style="font-family:courier new,courier,monospace">.cshrc/.tcshrc</span> for <span style="font-family:courier new,courier,monospace">tcsh</span>) you should use a command analogous to:</p>
<pre>source /usr/local/gromacs/bin/GMXRC</pre>
<p>near the end of that file.</p>"<br>can any one please tell me what is this..<br><br>nirmal<br><br><div class="gmail_quote">On Mon, Jan 9, 2012 at 1:48 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left:1px solid rgb(204,204,204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex"><div class="im">On 9/01/2012 6:54 PM, Nirmal Prasad wrote:<br>
<blockquote class="gmail_quote" style="border-left:1px solid rgb(204,204,204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex">
Dear Mark,<br>
<br>
Thanks for responding.<br>
<br>
I am new to Gromacs.<br>
<br>
I am working on Cytochrome P 450 proteins, these proteins contain HEME group.<br>
<br>
For MD run should I prepare separate protein and HEME group topologies<br>
and reconstruct protein-HEME complex. Is this procedure is correct or<br>
not.<br>
</blockquote>
<br></div>
A [moleculetype] cannot have covalent bonds with atoms outside itself. So whether your HEME group bonds covalently determines what can be found in a [moleculetype].<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div class="HOEnZb"><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="border-left:1px solid rgb(204,204,204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex">
<br>
nirmal<br>
<br>
<br>
<br>
On 1/9/12, Mark Abraham<<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.<u></u>au</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left:1px solid rgb(204,204,204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex">
On 9/01/2012 6:42 PM, Nirmal Prasad wrote:<br>
<blockquote class="gmail_quote" style="border-left:1px solid rgb(204,204,204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex">
Hello,<br>
<br>
I am working on Heme containing proteins, is it necessary to treat<br>
Heme group as Ligand.<br>
</blockquote>
What do you mean by "treating as a ligand"?<br>
<br>
Mark<br>
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