bharat gupta wrote:
does the gromacs force field has topology and ff parameter for H2PO4(-)
ion . As I have derived both topology and FF parameter from prodrug
Probably not; check the .rtp file for your desired force field.
server and after checking the topology I found that it has deleted of
the hydrogen.
See the PRODRG FAQ; this gets asked all the time.
http://davapc1.bioch.dundee.ac.uk/prodrg/prodrg_faq.html
No matter what PRODRG gives you, the charges will probably be useless anyway:
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
So you're in for the difficult process of parameterization if no one's already
developed parameters for your molecule:
http://www.gromacs.org/Documentation/How-tos/Parameterization
-Justin
On Thu, Jun 9, 2011 at 10:16 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
bharat gupta wrote:
Hi Justin,
I am having following doubts regarding umbrella sampling of
phosphate ion binding to my protein .
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.
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.
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).
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.
-Justin
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==============================__==========
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Virginia Tech
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jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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