<div dir="rtl"><div dir="ltr">Ho THANKS<br>MANY THANKS<br><br>I'm sorry, I'm new to Gromacs, and finally got it. Thank you very much.<br><br>Hagit.<br></div><div><br><div class="gmail_quote"><div dir="ltr">2012/5/2 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span></div>
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On 2/05/2012 8:55 PM, Hagit G wrote:
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<pre style="font-family:arial,helvetica,sans-serif"><font>Hi gmx users,</font></pre>
<font><br style="font-family:arial,helvetica,sans-serif">
<span style="font-family:arial,helvetica,sans-serif">Well, I
saw this question but the answer was not understood.</span><br style="font-family:arial,helvetica,sans-serif">
<span style="font-family:arial,helvetica,sans-serif">I'm
trying to work with the file 1PPB.pdb. There are 2 chains
connected with a disulfide bond. Gromacs automatically
adds H atoms.</span><br style="font-family:arial,helvetica,sans-serif">
<span style="font-family:arial,helvetica,sans-serif">Although
the disulfide bond is there, Gromacs ignore it because <b>each
cystein is on a different chain</b>. So it adds H and
therefor the disulfide bond is ruined during energy
minimization.</span><br style="font-family:arial,helvetica,sans-serif">
<span style="font-family:arial,helvetica,sans-serif">Is
there any way to recreate such a disulfide bond (Please
don't tell me again about "-ss" it works only on one
chain. Moreover, the bond is existed on the pdf file.) or
never ruined it at the first place?</span></font><br>
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Yes, and the clue to how to combine the chains to give the mechanism
a chance of working is on the page I linked last time: <a href="http://www.gromacs.org/Documentation/How-tos/Making_Disulfide_Bonds" target="_blank">http://www.gromacs.org/Documentation/How-tos/Making_Disulfide_Bonds</a><span class="HOEnZb"><font color="#888888"><br>
<br>
Mark<br>
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