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On 22/03/2012 1:46 AM, francesco oteri wrote:
<blockquote
cite="mid:CAFQcp-OOCADjH4Y8=LKqm7Vh9XfzO8QFGqzOisiMxhGFoGaT6Q@mail.gmail.com"
type="cite">Dear gromacs user,
<div>I noted a strange behavior in topology generation workflow.</div>
<div><br>
</div>
<div>I have a protein whose active site contains a Ni atom linked
to 4 Cys.</div>
<div>I inserted the 4 bonds by specbonds.dat. When I run
pdb2gmx, I have inspected</div>
<div>the Linking messages and they fit with the expected topology,
I mean pdb2gmx </div>
<div>correctly detects the four bonds nickel-sulphur. </div>
<div>So I run grompp and the topol.tpr has been
correctly generated.</div>
<div><br>
</div>
<div>Then I compared topol.top and topol.tpr bonds and I noticed
that in topol.top there a lot </div>
<div>of fake-bonds, i.e Ni-hydrogen, Ni-Carbonium. <br>
</div>
</blockquote>
<br>
Can you show an example of what you interpret as a fake bond?<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAFQcp-OOCADjH4Y8=LKqm7Vh9XfzO8QFGqzOisiMxhGFoGaT6Q@mail.gmail.com"
type="cite">
<div><br>
</div>
<div>I dumped topol.tpr through gmxdump, and I noticed that these
bonds are no more present</div>
<div>and only "right" bonds are present.</div>
<div><br>
</div>
<div>So, I am wondering why the fake bonds are inserted in
topol.top and how grompp detectes</div>
<div>these bonds.</div>
<div><br>
</div>
<div><br>
</div>
<div>Francesco</div>
<br>
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<br>
</blockquote>
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