Mark,<br><br><br>Also I'd like to know some more about most correct parametrisation of such new edited system. My new system consist of two proteins ( one- wich was initially and the second small peptide wich I've docked to the first protein). So now I need to define 2 separate groups for the below enties of my MD files<br>
<br><font face="Arial"><font size="3"><code>energygrps = Protein peptide<br></code></font></font><pre>tc-grps = Protein_Bilayer SOL_ions_peptide<br><br>and finally CoM groups because of the general anisotropy of the membrane system<br>
<br>comm-grps = Protein_Bilayer SOL_Ions_Peptide<br><br>I've made itp file for the peptide via pdb2gmx so in th default definition both the protein and peptide are the protein enty in the index file.<br><br>I've separate both of the protein and peptide by selection of two subsets of atoms wich represent to the each of that enties.<br>
<br>So finally I have two groups in the index.ndx file<br><br>a_1-5000 ( it's protein)<br>a_9999-10500 (it's peptide)<br><br>Does this separation correct in general ? I have some fears because both protein and peptide consist of the same residue numbers in the GRO file ( e.g there are 212- lys wich is part of the protein and 212-Pro wich is part of the peptide ) Might this system be tended to errors?<br>
I have no errors during processing of that sustem by grompp as well as md run. What should I do for such system consisted of two proteins in separate phases ( membrane-like and water)<br>?<br><br>Thanks for help again,<br>
<br>James <br></pre><br><font face="Arial"><font size="3"><code><br></code></font></font><br><div class="gmail_quote">30 марта 2012 г. 17:34 пользователь Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> написал:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Constructing a system is normally easiest if you remove all your solvent(s), paste in your interesting molecules somehow or other, and then rebuild the solvent with tools like genbox.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark<br>
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