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 ?? <br><br><div class="gmail_quote">On Thu, Jun 9, 2011 at 10:26 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">
does the gromacs force field has topology and ff parameter for H2PO4(-) ion . As I have derived both topology and FF parameter from prodrug <br>
</blockquote>
<br></div>
Probably not; check the .rtp file for your desired force field.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
server and after checking the topology I found that it has deleted of the hydrogen.<br>
<br>
</blockquote>
<br></div>
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.<u></u>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/<u></u>Downloads/Related_Software/<u></u>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/<u></u>Documentation/How-tos/<u></u>Parameterization</a><br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div></div><div class="h5">
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>
-- ==============================<u></u>__==========<br>
<br>
Justin A. Lemkul<br>
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ICTAS Doctoral Scholar<br>
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Department of Biochemistry<br>
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-- <br>
Bharat<br>
Ph.D. Candidate<br>
Room No. : 7202A, 2nd Floor<br>
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<br>
</blockquote><div><div></div><div class="h5">
<br>
-- <br>
==============================<u></u>==========<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>
<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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</div></div></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>