<br><br><div class="gmail_quote">On Thu, May 24, 2012 at 3:42 PM, Steven Neumann <span dir="ltr"><<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gmx Users,<br><br>I want to use distance restraints of 3 atoms which belong to 3 different proteins. For this purpose I want to create one topology so one moleculetype: <br><br>I tried to use pdb2gmx -chainsep ter (where i put TER after each chain in my PDB)<br>
<br>But 3 separate topologies were created. <br><br>I want to adjust proper charges for each teraminals but pdb2gmx without -chainsep will treat it as a one molecule.<br><br>Please help.<span class="HOEnZb"><font color="#888888"><br>
<br>Steven<br><br><br>
</font></span></blockquote></div><br>It is stated:<br><br>The separation of chains is not entirely trivial since the markup in<br>user-generated PDB files frequently varies and sometimes it is desirable to<br>merge entries across a TER record, for instance if you want a disulfide<br>
bridge or <u>distance restraints</u> between two protein chains or if you have a<br>HEME group bound to a protein. In such cases multiple chains should be<br>contained in a single molecule_type definition. To handle this, pdb2gmx has<br>
an option -chainsep so you can choose whether a new chain should start when<br>we find a TER record, when the chain id changes, combinations of either or<br>both of these or fully interactively.<br><br>And if I use:<br><br>
pdb2gmx -chainsep <br><br>In my topology:<br><br>; Include chain topologies<br>#include "topol_Protein.itp"<br>#include "topol_Protein2.itp"<br>#include "topol_Protein3.itp"<br><br><br><br>[ molecules ]<br>
; Compound #mols<br>Protein 1<br>Protein2 1<br>Protein3 1<br><br><br>So how can I have one [moleculetype] for the usage of distance restraints? Why do they state that this option will allow to have one [moleculetype] ?<br>
<br>Please, help<br><br>Steven<br><br>