<span class="Apple-style-span" style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; "> 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>
</span><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">bharat gupta</b> <span dir="ltr"><<a href="mailto:bharat.85.monu@gmail.com">bharat.85.monu@gmail.com</a>></span><br>
Date: Fri, Jun 17, 2011 at 11:18 AM<br>Subject: Re: [gmx-users] Re: Gromacs error<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br><br><br>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>
<br><br><div class="gmail_quote"><div><div></div><div class="h5">On Fri, Jun 17, 2011 at 10:04 AM, Dallas Warren <span dir="ltr"><<a href="mailto:Dallas.Warren@monash.edu" target="_blank">Dallas.Warren@monash.edu</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div></div><div class="h5">
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<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">Someone with some more in depth knowledge will hopefully pipe up, but until then there are some things you can read up on and see if it will solve your issue.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">Google is your friend.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">Put “error while loading shared libraries: libgmx.so.6: Permission denied” into it, and you get a number of topics on forums discussing the issue you have
had. Not directly with libgmx.so.6 but that issue appears to be the same. And they all relate to Fedora from what I can see.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">This one appears to solve the issue -
<a href="http://forums.fedoraforum.org/showthread.php?t=253870" target="_blank">http://forums.fedoraforum.org/showthread.php?t=253870</a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D">With some more reading you should be able to sort out what the issue actually is, seems to be something to do with how files are handled with Fedora, and then
the correct course of action.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">Catch ya,<br>
<br>
Dr. Dallas Warren<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">Medicinal Chemistry and Drug Action<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">Monash Institute of Pharmaceutical Sciences</span><span style="font-size:10.0pt;color:#1F497D">, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<a href="mailto:dallas.warren@monash.edu" target="_blank">dallas.warren@monash.edu</a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">+61 3 9903 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a nail.</span><span style="font-size:11.0pt;color:#1F497D">
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"><u></u> <u></u></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt">From:</span></b><span style="font-size:10.0pt"> <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>]
<b>On Behalf Of </b>bharat gupta<br>
<b>Sent:</b> Friday, 17 June 2011 10:40 AM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> [gmx-users] Re: Gromacs error<u></u><u></u></span></p>
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<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">Hi,<br>
<br>
I have installed gromacs 4.5 on fedora core 15 and whenever I try to run any command like pdb2gmx ... I am getting the following error :<br>
<br>
error while loading shared libraries: libgmx.so.6: cannot enable executable stack as shared object requires: Permission denied<br>
<br>
Pls help??<br>
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<br>
-- <br>
Bharat<u></u><u></u></p>
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</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>
Busan -609735<br>South Korea<br>Lab phone no. - +82-51-510-3680, +82-51-583-8343<div>Mobile no. - 010-5818-3680<br>E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div><br>