does the gromacs force field has topology and ff parameter for H2PO4(-) ion . As I have derived both topology and FF parameter from prodrug server and after checking the topology I found that it has deleted of the hydrogen.<br>
<br><div class="gmail_quote">On Thu, Jun 9, 2011 at 10:16 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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"><br>
<br>
bharat gupta wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Justin,<br>
<br>
I am having following doubts regarding umbrella sampling of phosphate ion binding to my protein .<br>
<br>
1. As per the tutorial, I need to fix an immobile reference. In my case which region do I have to fix as my protein consists of one single chain. Since I am studying the binding and unbinding of ion, shall I fix the ion fixed. If it's so, then do I have to give a different chain name for it as my complex doesnot chain name for ion/ligand.<br>
<br>
</blockquote>
<br></div>
You don't need an immobile reference just because my tutorial did. I had a particular need to do so. For your purpose, I highly doubt it's necessary. You're looking at small molecule-protein interactions, not protein-protein interactions.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
2. What should be the size of box and how do I know where to place the protein's COM in box (the precise location).<br>
<br>
</blockquote>
<br></div>
The absolute COM is somewhat irrelevant; all distances during pulling are relative. You can place the protein in a certain location in the box for convenience if you like. The box size must be greater than twice the pull distance, as explained in the tutorial. The amount that you wish to pull will dictate both the location of the protein and the box size.<br>
<br>
-Justin<br>
<br>
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Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
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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>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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</font></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>
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>