Tahnk you both. Indeed, it works so -chainsep interactive <br><br>Steven<br><br><div class="gmail_quote">On Thu, May 24, 2012 at 9:44 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">Okay,okay, I give in. To settle this again, I looked it up, and among<br>
the options to -chainsep is 'interactive'. If you use that you're<br>
prompted whether or not to separate at the breaks pdb2gmx detects.<br>
That allows you to merge chains. I guess there'd be sense in just<br>
having an option 'no' to merge everything, but that's for the<br>
developers to pick up ;)<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<div class="HOEnZb"><div class="h5"><br>
On Thu, May 24, 2012 at 10:28 PM, Francesca<br>
<<a href="mailto:francesca.stanzione@unina.it">francesca.stanzione@unina.it</a>> wrote:<br>
> I had the same problem and I didn't find any way to do it. So i created new<br>
> residues for the terminals, and I added them to the forcefields files.<br>
> Example: if my first COOH terminal was a SER i created a SERT residues and I<br>
> used the COOH values taken from ASP , and the same procedure was used for<br>
> the next Nterminal...in that way I have a SERT in the list of amminoacids<br>
> and when you process the pdb2gmx you have 1moleculetype, but you have 3<br>
> different chains each with its terminals. Be careful to use correct values<br>
> and add these residues to the list of amminoacids in the forcefield<br>
> directory. I used that method and I could apply the distance restraints.<br>
><br>
> Cheers,<br>
> Francesca<br>
><br>
> --<br>
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<br>
</div></div><div class="im HOEnZb">--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
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