<br><br><div class="gmail_quote">On Thu, May 24, 2012 at 6:05 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<p>Hi Steven,</p>
<p>Doesn't -chainsep take an argument?</p>
<p>Cheers,</p>
<p>Tsjerk</p></blockquote><div><br>It does, I used option: -chainsep ter<br>And I had in my pdb file after each chain TER and thus 3 itp files were created corresponding to my top file and representing different moleculetype (protein, protein2, protein3). In order to use distance restraints I want to have one moleculetype with 3 chains which are not connected via bonds and adjust proper charges to each of 6 terminals. Any suggestions?<br>
<br>Steven <br></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<p></p><blockquote type="cite">On May 24, 2012 5:33 PM, "Steven Neumann" <<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>> wrote:<br><br><p><font color="#500050">
On Thu, May 24, 2012 at 3:42 PM, Steven Neumann <<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>> wrote:
>
> Dear Gmx Users,...</font></p><div><div class="h5">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<font color="#888888"><br><br>Steven<br><br>
</font><br></div></div><span class="HOEnZb"><font color="#888888">--<br>
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