I took all the parameters of Ptyr from amber parameter database and followed what was said in the documentation. Shall mail the changes made for topology<br><br><div class="gmail_quote">On Fri, Jun 17, 2011 at 5:17 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im">On 06/17/2011 12:18 PM, bharat gupta wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
thanks.. I fixed the problem by using the command execstack -c filename<br>
<br>
<br>
but I have another issue .. I am am preparing the structure for simulation which is a docked complex containing Phospharylated tyrosine. I am using Amber 99 force field and update the residuetypes.dat, aminoacid.rtp, ffbonded.itp files for pTYR but still the error that "Residue 'PTYR' not found in residue topology database" ... but all the changes I have made then where else could the problem be ??<br>
</blockquote>
<br></div>
Isn't it rather more likely your error is in something you've already done? Be sure you have followed <a href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field" target="_blank">http://www.gromacs.org/<u></u>Documentation/How-tos/Adding_<u></u>a_Residue_to_a_Force_Field</a><br>
<br>
Mark<br><font color="#888888">
-- <br></font><div><div></div><div class="h5">
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Bharat<br>Ph.D. Candidate<br>Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>Pusan National University<br>
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