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On 2/12/2011 3:41 PM, bharat gupta wrote:
<blockquote
cite="mid:CAAh+zSXhXu1BrL4yby8YuDgwmDTw9ceQtOdiN2AFpdNR5JkDtQ@mail.gmail.com"
type="cite">Yes, but I took the coordinates for phosphate ion from
some other pdb file and docked with my protein using autodock.
Then I generated the parameter for the ion using swissparam. Then
prepared the protein file using pdb2gmx and pasted the coordinates
of docked ion from the docked file obtained from autodock. What
Shall I do now ?? ... <br>
</blockquote>
<br>
Don't paste apples with oranges and feed them to a program in a
format that specifies only apples. Convert the units.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAAh+zSXhXu1BrL4yby8YuDgwmDTw9ceQtOdiN2AFpdNR5JkDtQ@mail.gmail.com"
type="cite">
<br>
<div class="gmail_quote">On Fri, Dec 2, 2011 at 1:35 PM, Dallas
Warren <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Dallas.Warren@monash.edu">Dallas.Warren@monash.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div link="blue" vlink="purple" lang="EN-US">
<div>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">One
file you used had the coordinates in angstroms, the
other in nanometers.</span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">You
cannot have numbers with different units in the same
coordinate file. Which is what you did. Hence why
they are not in the locations you assumed they were.</span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Catch
ya,<br>
<br>
Dr. Dallas Warren</span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Medicinal
Chemistry and Drug Action</span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Monash
Institute of Pharmaceutical Sciences</span><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d">,
Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<a moz-do-not-send="true"
href="mailto:dallas.warren@monash.edu"
target="_blank">dallas.warren@monash.edu</a></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif";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;font-family:"Calibri","sans-serif";color:#1f497d"></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<div style="border:none;border-left:solid blue
1.5pt;padding:0cm 0cm 0cm 4.0pt">
<div>
<div style="border:none;border-top:solid #b5c4df
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">
<a moz-do-not-send="true"
href="mailto:gmx-users-bounces@gromacs.org"
target="_blank">gmx-users-bounces@gromacs.org</a>
[mailto:<a moz-do-not-send="true"
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, 2 December 2011 3:22 PM<br>
<b>To:</b> <a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>;
Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] Re: Protein
ligand simulation</span></p>
</div>
</div>
<div class="im">
<p class="MsoNormal"> </p>
<p class="MsoNormal" style="margin-bottom:12.0pt">I
didn't understand what you meant by that link. Can
you please tell me what can be done ??</p>
</div>
<div>
<div class="h5">
<div>
<p class="MsoNormal">On Fri, Dec 2, 2011 at 11:52
AM, Justin A. Lemkul <<a
moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>
wrote:</p>
<div>
<p class="MsoNormal"><br>
<br>
bharat gupta wrote:</p>
<p class="MsoNormal"
style="margin-bottom:12.0pt">Sorry I didn't
understand . Can u brief it ??</p>
<p class="MsoNormal"> </p>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt">I
already did:<br>
<br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/pipermail/gmx-users/2011-December/066664.html"
target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2011-December/066664.html</a><br>
<br>
-Justin</p>
<div>
<p class="MsoNormal"
style="margin-bottom:12.0pt">On Fri, Dec 2,
2011 at 11:47 AM, Justin A. Lemkul <<a
moz-do-not-send="true"
href="mailto:jalemkul@vt.edu"
target="_blank">jalemkul@vt.edu</a>
<mailto:<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu"
target="_blank">jalemkul@vt.edu</a>>>
wrote:<br>
<br>
<br>
<br>
bharat gupta wrote:<br>
<br>
Yes, I prepared the protein file
separately using pdb2gmx and<br>
then I pasted the ligand manually from
the docked file.<br>
<br>
<br>
Then you prepared it incorrectly. You need
to use the right units.<br>
<br>
-Justin<br>
<br>
</p>
</div>
<p class="MsoNormal"> --
==============================__==========</p>
<div>
<p class="MsoNormal"><br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA</p>
</div>
<div>
<p class="MsoNormal"> jalemkul[at]<a
moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> <<a
moz-do-not-send="true" href="http://vt.edu"
target="_blank">http://vt.edu</a>> |
(540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem."
target="_blank">http://www.bevanlab.biochem.</a>__<a
moz-do-not-send="true"
href="http://vt.edu/Pages/Personal/justin"
target="_blank">vt.edu/Pages/Personal/justin</a><br>
<<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a>><br>
<br>
==============================__==========</p>
</div>
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<br>
<br>
<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<br>
Mobile no. - 010-5818-3680</p>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt">E-mail
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monu46010@yahoo.com</a> <mailto:<a
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<div>
<p class="MsoNormal"><br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true"
href="http://vt.edu" target="_blank">vt.edu</a>
| (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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<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</p>
<div>
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<br>
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<div><br>
</div>
-- <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 moz-do-not-send="true"
href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div>
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</blockquote>
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