Yes, I read the prodrug faqs... then in that case I have to parametrize the ion ... According to you there is no other way of doing it ??<br><br><div class="gmail_quote">On Thu, Jun 9, 2011 at 10:30 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><div></div><div class="h5"><br>
<br>
bharat gupta wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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>
</blockquote>
<br></div></div>
Not likely. Please read in the manual about why the gmx.ff force field should not be used.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
On Thu, Jun 9, 2011 at 10:26 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></div><div class="im">
does the gromacs force field has topology and ff parameter for<br>
H2PO4(-) ion . As I have derived both topology and FF parameter<br>
from prodrug<br>
<br>
<br>
Probably not; check the .rtp file for your desired force field.<br>
<br>
<br>
server and after checking the topology I found that it has<br>
deleted of the hydrogen.<br>
<br>
<br>
See the PRODRG FAQ; this gets asked all the time.<br>
<br>
<a href="http://davapc1.bioch.dundee." target="_blank">http://davapc1.bioch.dundee.</a>__<a href="http://ac.uk/prodrg/prodrg_faq.html" target="_blank"><u></u>ac.uk/prodrg/prodrg_faq.html</a><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<br>
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>
<<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<br>
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>
<<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>
On Thu, Jun 9, 2011 at 10:16 AM, Justin A. Lemkul<br>
<<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>><br></div><div><div></div><div class="h5">
<mailto:<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<br>
reference. In<br>
my case which region do I have to fix as my protein<br>
consists of<br>
one single chain. Since I am studying the binding and<br>
unbinding<br>
of ion, shall I fix the ion fixed. If it's so, then do I<br>
have to<br>
give a different chain name for it as my complex doesnot<br>
chain<br>
name for ion/ligand.<br>
<br>
<br>
You don't need an immobile reference just because my tutorial<br>
did.<br>
I had a particular need to do so. For your purpose, I<br>
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<br>
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>
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