<br>Yes, you are right, the chromophore(p-coumaric acid) is covalently bonded to the Sulphur(S) atom of the Cys-69 residue.<br>But I specified the covalent bond in my topology.<br><br>[ bonds]<br> C +SG<br><br>[ angles ]<br>
O C +SG <br> CA1 C +SG <br> C +SG +CB <br><br>[ dihedrals ]<br> O C +SG +CB<br> CA1 C +SG +CB<br> HA2 CA1 C +SG<br> CA2 CA1 C +SG<br> C +SG +CB +CA<br>
C +SG +CB +HB1<br> C +SG +CB +HB2<br><br>After doing pdb2gmx, i got the right structure. But the chromophore flies away after minimising. <br><br><br>Thanks<br>Rama<br><br><div class="gmail_quote">On Wed, Apr 20, 2011 at 4:57 PM, Peter C. Lai <span dir="ltr"><<a href="mailto:pcl@uab.edu">pcl@uab.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Isn't the chromophore supposed to be covalently bonded to the protein?<br>
My cursory search shows Vengris et al 2004 in Biophys. J. citing Baca et al<br>
1994 and van Beeumen et al 1993: "This small 125-residue protein contains a<br>
p-coumaric acid chromophore that is covalently bound to the protein backbone<br>
via a thiol-ester cysteine linkage Cys-69"...<br>
<br>
Maybe you forgot to specify a covalent bond in your topology...<br>
<div><div></div><div class="h5"><br>
On 2011-04-20 06:46:54PM -0500, Ramachandran G wrote:<br>
> Hi gromacs users,<br>
> I am working on Photo active yellow protein.<br>
><br>
> Although i successfully build the force field and patched the chromophore to the protein.<br>
> After energy minimizing the protein, the chromophore flies away separately. I don't know whether i am missing anything?<br>
> Please help.<br>
> Rama<br>
><br>
><br>
<br>
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Peter C. Lai | University of Alabama-Birmingham<br>
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