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On 06/17/2011 06:36 PM, bharat gupta wrote:
<blockquote
cite="mid:BANLkTik5Pox1mZGHWsAKfRWcyam6Z37Hfg@mail.gmail.com"
type="cite">I took all the parameters of Ptyr from amber parameter
database and followed what was said in the documentation.</blockquote>
<br>
The fact that you seem to change the capitalization of "PTYR" every
time you type it does not inspire confidence that you've taken due
care of all the details required.<br>
<br>
<blockquote
cite="mid:BANLkTik5Pox1mZGHWsAKfRWcyam6Z37Hfg@mail.gmail.com"
type="cite"> Shall mail the changes made for topology<br>
</blockquote>
<br>
I don't have time to sift through them. Try using the diff tool to
compare before and after so that you can verify that your mental
picture of what you have done agrees with what you have done.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTik5Pox1mZGHWsAKfRWcyam6Z37Hfg@mail.gmail.com"
type="cite">
<div class="gmail_quote">On Fri, Jun 17, 2011 at 5:17 PM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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;">
<div class="im">On 06/17/2011 12:18 PM, bharat gupta wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
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
moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field"
target="_blank">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a><br>
<br>
Mark<br>
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</blockquote>
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<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>
Busan -609735<br>
South Korea<br>
Lab phone no. - +82-51-510-3680, +82-51-583-8343
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