[gmx-users] Umbrella sampling of phosphate ion binding

[Justin A. Lemkul]

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 <jalemkul at vt.edu 
> <mailto:jalemkul at 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
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>     ==============================__==========
>     -- 
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/__mailman/listinfo/gmx-users
>     <http://lists.gromacs.org/mailman/listinfo/gmx-users>
>     Please search the archive at
>     http://www.gromacs.org/__Support/Mailing_Lists/Search
>     <http://www.gromacs.org/Support/Mailing_Lists/Search> before posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
>     <http://www.gromacs.org/Support/Mailing_Lists>
> 
> 
> 
> 
> -- 
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
> 

-- 
========================================

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

========================================