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On 4/21/2011 10:12 AM, Ramachandran G wrote:
<blockquote
cite="mid:BANLkTimKK5VRG01aWwSDBVLFANSgckx7eQ@mail.gmail.com"
type="cite"><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>
</blockquote>
<br>
That's your .rtp entry. What's in your [molecules] section of your
topology?<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTimKK5VRG01aWwSDBVLFANSgckx7eQ@mail.gmail.com"
type="cite"><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 moz-do-not-send="true"
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 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>
</div>
</div>
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<font color="#888888"><br>
<br>
--<br>
===============================================================<br>
Peter C. Lai | University of
Alabama-Birmingham<br>
Programmer/Analyst | BEC 257<br>
Genetics, Div. of Research | 1150 10th Avenue South<br>
<a moz-do-not-send="true" href="mailto:pcl@uab.edu">pcl@uab.edu</a>
| Birmingham AL 35294-4461<br>
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value="+12056900808">(205) 690-0808</a> |<br>
===============================================================<br>
<br>
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