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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">You have been provided there with the reference in which the parameters for the molecule were derived.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Read it!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">And determine yourself if it is applicable or not to what you are doing and the forcefield you are using.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></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<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Medicinal Chemistry and Drug Action<o:p></o:p></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>
dallas.warren@monash.edu<o:p></o:p></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">
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<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""> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org]
<b>On Behalf Of </b>bharat gupta<br>
<b>Sent:</b> Thursday, 9 June 2011 11:29 AM<br>
<b>To:</b> jalemkul@vt.edu; Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] Umbrella sampling of phosphate ion binding<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">I found it in the /shared/top/ gmx.ff folder . Here's the file<br>
<br>
;<br>
; Force field based on GROMOS with new charges as described in<br>
; D. van der Spoel, K.A. Feenstra, M.A. Hemminga and H.J.C. Berendsen: <br>
; Molecular modeling of the RNA binding N-terminal part of cowpea chlorotic <br>
; mottle virus coat protein in solution with phosphate ions <br>
; Biophys. J. 71 pp. 2920-2932 (1996)<br>
;<br>
[ moleculetype ]<br>
; name nrexcl<br>
h2po4 4<br>
<br>
[ atoms ]<br>
; nr type resnr residu atom cgnr charge mass<br>
; use charges from Janez Mavri<br>
1 OA 1 PI O1 1 -0.777<br>
2 OA 1 PI O2 1 -0.777<br>
3 OM 1 PI O3 1 -0.943<br>
4 OM 1 PI O4 1 -0.943<br>
5 P 1 PI P 1 1.596<br>
6 HO 1 PI H1 1 0.422<br>
7 HO 1 PI H2 1 0.422<br>
<br>
[ bonds ]<br>
; ai aj funct c0 c1<br>
5 1 1 1.637000e-01<br>
5 2 1 1.637000e-01<br>
5 3 1 1.478000e-01<br>
5 4 1 1.478000e-01<br>
6 1 1 0.943000e-01<br>
7 2 1 0.943000e-01<br>
<br>
[ angles ]<br>
; ai aj ak funct c0 c1<br>
2 5 1 1 1.015000e+02 400<br>
3 5 1 1 1.059000e+02<br>
4 5 1 1 1.082000e+02<br>
3 5 2 1 1.059000e+02<br>
4 5 2 1 1.082000e+02<br>
4 5 3 1 1.248000e+02<br>
6 1 5 1 1.082000e+02<br>
7 2 5 1 1.082000e+02<br>
<br>
[ dihedrals ]<br>
; ai aj ak al funct<br>
6 1 5 2 1<br>
7 2 5 1 1<br>
<br>
Can I use it or not ?? <o:p></o:p></p>
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<p class="MsoNormal">On Thu, Jun 9, 2011 at 10:26 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<o:p></o:p></p>
<div>
<p class="MsoNormal"><br>
<br>
bharat gupta wrote:<o:p></o:p></p>
<p class="MsoNormal">does the gromacs force field has topology and ff parameter for H2PO4(-) ion . As I have derived both topology and FF parameter from prodrug
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal">Probably not; check the .rtp file for your desired force field.<o:p></o:p></p>
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<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm">
<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">server and after checking the topology I found that it has deleted of the hydrogen.<o:p></o:p></p>
</blockquote>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">See the PRODRG FAQ; this gets asked all the time.<br>
<br>
<a href="http://davapc1.bioch.dundee.ac.uk/prodrg/prodrg_faq.html" target="_blank">http://davapc1.bioch.dundee.ac.uk/prodrg/prodrg_faq.html</a><br>
<br>
No matter what PRODRG gives you, the charges will probably be useless anyway:<br>
<br>
<a href="http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips" target="_blank">http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips</a><br>
<br>
So you're in for the difficult process of parameterization if no one's already developed parameters for your molecule:<br>
<br>
<a href="http://www.gromacs.org/Documentation/How-tos/Parameterization" target="_blank">http://www.gromacs.org/Documentation/How-tos/Parameterization</a><br>
<br>
-Justin<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal">On Thu, Jun 9, 2011 at 10:16 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
bharat gupta wrote:<br>
<br>
Hi Justin,<br>
<br>
I am having following doubts regarding umbrella sampling of<br>
phosphate ion binding to my protein .<br>
<br>
1. As per the tutorial, I need to fix an immobile reference. In<br>
my case which region do I have to fix as my protein consists of<br>
one single chain. Since I am studying the binding and unbinding<br>
of ion, shall I fix the ion fixed. If it's so, then do I have to<br>
give a different chain name for it as my complex doesnot chain<br>
name for ion/ligand.<br>
<br>
<br>
You don't need an immobile reference just because my tutorial did.<br>
I had a particular need to do so. For your purpose, I highly doubt<br>
it's necessary. You're looking at small molecule-protein<br>
interactions, not protein-protein interactions.<br>
<br>
<br>
2. What should be the size of box and how do I know where to<br>
place the protein's COM in box (the precise location).<br>
<br>
<br>
The absolute COM is somewhat irrelevant; all distances during<br>
pulling are relative. You can place the protein in a certain<br>
location in the box for convenience if you like. The box size must<br>
be greater than twice the pull distance, as explained in the<br>
tutorial. The amount that you wish to pull will dictate both the<br>
location of the protein and the box size.<br>
<br>
-Justin<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<o:p></o:p></p>
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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>
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-- <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 href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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-- <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>
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