<p>Hi Steven,</p>
<p>There will be three dihedrals spanning a break. Make sure to remove all of them. Of course pdb2gmx shouldn't just connect the chain ends... Maybe you can file it as a bug.</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On May 25, 2012 3:11 PM, "Steven Neumann" <<a href="mailto:s.neumann08@gmail.com">s.neumann08@gmail.com</a>> wrote:<br><br>Yes, it works (-chainsep interactive: merge = yes ) but when you process to grompp there is an error:<br>
<br>Unknown cmap torsion between atoms 6002 6004 6006 6017 6021<br><br>pdb2gmx
takes the cmap for the atoms e.g. last two residues of chain A with
first three residues of chain B. Removing these lines does not solve the problem. Any suggestions appreciated!<br><br> <br><br><div class="gmail_quote">On Fri, May 25, 2012 at 9:57 AM, 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"><br><br><div class="gmail_quote"><p><font color="#500050">> On Thu, May 24, 2012 at 10:04 PM, Francesca <<a href="mailto:francesca.stanzione@unina.it">francesca.stanzione@unina.it</a>> wrote:
>>
>> I checked ...</font></p><div><br>Yes, it works (-chainsep interactive: merge = no ) but when you process to grompp there is an error:<br><br>Unknown cmap torsion between atoms 6002 6004 6006 6017 6021<br><br>pdb2gmx takes the cmap for the atoms e.g. last two residues of chain A with first three residues of chain B. Does removing this lines will be reasonable or some torsions wont be taken into account?<span><font color="#888888"><br>
<br>Steven<br><br></font></span></div><p><font color="#500050">>>
>>
>> --
>> View this message in context: <a href="http://gromacs.5086.n6.nabble.com/One-molculetype-for-3.">http://gromacs.5086.n6.nabble.com/One-molculetype-for-3.</a>..</font></p></div><br>
</blockquote></div><br>
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